diff --git a/deploy.sh b/deploy.sh
index 7ed8d88..fa5e43c 100755
--- a/deploy.sh
+++ b/deploy.sh
@@ -35,6 +35,7 @@ REMOTE_COPY_SOURCE=0
 REMOTE_ARGS_PROVIDED=0
 REMOTE_AUTO_DEPLOY=0
 REMOTE_AUTO_DEPLOY=0
+REMOTE_CLEAN_RUNTIME=0
 REMOTE_STORAGE_OVERRIDE=""
 REMOTE_CONTAINER_USER_OVERRIDE=""
 REMOTE_ENV_FILE=""
@@ -168,6 +169,16 @@ collect_remote_details(){
     esac
   fi
 
+  if [ "$interactive" -eq 1 ] && [ "$REMOTE_ARGS_PROVIDED" -eq 0 ]; then
+    local cleanup_answer
+    read -rp "Stop/remove remote containers & project images during migration? [y/N]: " cleanup_answer
+    cleanup_answer="${cleanup_answer:-n}"
+    case "${cleanup_answer,,}" in
+      y|yes) REMOTE_CLEAN_RUNTIME=1 ;;
+      *) REMOTE_CLEAN_RUNTIME=0 ;;
+    esac
+  fi
+
   # Optional remote env overrides (default to current values)
   local storage_default container_user_default
   storage_default="$(read_env STORAGE_PATH "./storage")"
@@ -240,6 +251,7 @@ Options:
   --remote-skip-storage                    Skip syncing the storage directory during migration
   --remote-copy-source                     Copy the local project directory to remote instead of relying on git
   --remote-auto-deploy                     Run './deploy.sh --yes --no-watch' on the remote host after migration
+  --remote-clean-runtime                   Stop/remove remote containers & project images during migration
   --remote-storage-path PATH               Override STORAGE_PATH/STORAGE_PATH_LOCAL in the remote .env
   --remote-container-user USER[:GROUP]     Override CONTAINER_USER in the remote .env
   --skip-config                            Skip applying server configuration preset
@@ -270,6 +282,7 @@ while [[ $# -gt 0 ]]; do
     --remote-skip-storage) REMOTE_SKIP_STORAGE=1; REMOTE_MODE=1; REMOTE_ARGS_PROVIDED=1; shift;;
     --remote-copy-source) REMOTE_COPY_SOURCE=1; REMOTE_MODE=1; REMOTE_ARGS_PROVIDED=1; shift;;
     --remote-auto-deploy) REMOTE_AUTO_DEPLOY=1; REMOTE_MODE=1; REMOTE_ARGS_PROVIDED=1; shift;;
+    --remote-clean-runtime) REMOTE_CLEAN_RUNTIME=1; REMOTE_MODE=1; REMOTE_ARGS_PROVIDED=1; shift;;
     --remote-storage-path) REMOTE_STORAGE_OVERRIDE="$2"; REMOTE_MODE=1; REMOTE_ARGS_PROVIDED=1; shift 2;;
     --remote-container-user) REMOTE_CONTAINER_USER_OVERRIDE="$2"; REMOTE_MODE=1; REMOTE_ARGS_PROVIDED=1; shift 2;;
     --skip-config) SKIP_CONFIG=1; shift;;
@@ -680,6 +693,10 @@ run_remote_migration(){
     args+=(--copy-source)
   fi
 
+  if [ "$REMOTE_CLEAN_RUNTIME" -eq 1 ]; then
+    args+=(--cleanup-runtime)
+  fi
+
   if [ "$ASSUME_YES" -eq 1 ]; then
     args+=(--yes)
   fi
diff --git a/docker-compose.yml b/docker-compose.yml
index 4e709d8..d9f2e22 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -557,7 +557,7 @@ services:
       AC_UPDATES_ENABLE_DATABASES: "7"
       AC_BIND_IP: "0.0.0.0"
       AC_DATA_DIR: "/azerothcore/data"
-      AC_SOAP_PORT: "7878"
+      AC_SOAP_PORT: "${SOAP_PORT}"
       AC_PROCESS_PRIORITY: "0"
       AC_ELUNA_ENABLED: "${AC_ELUNA_ENABLED}"
       AC_ELUNA_TRACE_BACK: "${AC_ELUNA_TRACE_BACK}"
@@ -688,7 +688,7 @@ services:
       AC_UPDATES_ENABLE_DATABASES: "7"
       AC_BIND_IP: "0.0.0.0"
       AC_DATA_DIR: "/azerothcore/data"
-      AC_SOAP_PORT: "7878"
+      AC_SOAP_PORT: "${SOAP_PORT}"
       AC_PROCESS_PRIORITY: "0"
       AC_ELUNA_ENABLED: "${AC_ELUNA_ENABLED}"
       AC_ELUNA_TRACE_BACK: "${AC_ELUNA_TRACE_BACK}"
@@ -744,7 +744,7 @@ services:
       AC_UPDATES_ENABLE_DATABASES: "7"
       AC_BIND_IP: "0.0.0.0"
       AC_DATA_DIR: "/azerothcore/data"
-      AC_SOAP_PORT: "7878"
+      AC_SOAP_PORT: "${SOAP_PORT}"
       AC_PROCESS_PRIORITY: "0"
       AC_ELUNA_ENABLED: "${AC_ELUNA_ENABLED}"
       AC_ELUNA_TRACE_BACK: "${AC_ELUNA_TRACE_BACK}"
diff --git a/scripts/bash/backup-export.sh b/scripts/bash/backup-export.sh
index 4af7f68..a83cf56 100755
--- a/scripts/bash/backup-export.sh
+++ b/scripts/bash/backup-export.sh
@@ -4,8 +4,17 @@ set -euo pipefail
 
 INVOCATION_DIR="$PWD"
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+PROJECT_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 cd "$SCRIPT_DIR"
 
+# Load environment defaults if present
+if [ -f "$PROJECT_ROOT/.env" ]; then
+  set -a
+  # shellcheck disable=SC1091
+  source "$PROJECT_ROOT/.env"
+  set +a
+fi
+
 SUPPORTED_DBS=(auth characters world)
 declare -A SUPPORTED_SET=()
 for db in "${SUPPORTED_DBS[@]}"; do
@@ -16,10 +25,12 @@ declare -A DB_NAMES=([auth]="" [characters]="" [world]="")
 declare -a INCLUDE_DBS=()
 declare -a SKIP_DBS=()
 
-MYSQL_PW=""
+MYSQL_PW="${MYSQL_ROOT_PASSWORD:-}"
 DEST_PARENT=""
 DEST_PROVIDED=false
 EXPLICIT_SELECTION=false
+MYSQL_CONTAINER="${CONTAINER_MYSQL:-ac-mysql}"
+DEFAULT_BACKUP_DIR="${BACKUP_PATH:-${STORAGE_PATH:-./storage}/backups}"
 
 usage(){
   cat <<'EOF'
@@ -28,7 +39,7 @@ Usage: ./backup-export.sh [options]
 Creates a timestamped backup of one or more ACore databases.
 
 Options:
-  -o, --output DIR          Destination directory (default: storage/backups)
+  -o, --output DIR          Destination directory (default: BACKUP_PATH from .env, fallback: ./storage/backups)
   -p, --password PASS       MySQL root password
       --auth-db NAME        Auth database schema name
       --characters-db NAME  Characters database schema name
@@ -224,13 +235,9 @@ done
 if $DEST_PROVIDED; then
   DEST_PARENT="$(resolve_relative "$INVOCATION_DIR" "$DEST_PARENT")"
 else
-  # Use storage/backups as default to align with existing backup structure
-  if [ -d "$SCRIPT_DIR/storage" ]; then
-    DEST_PARENT="$SCRIPT_DIR/storage/backups"
-    mkdir -p "$DEST_PARENT"
-  else
-    DEST_PARENT="$SCRIPT_DIR"
-  fi
+  DEFAULT_BACKUP_DIR="$(resolve_relative "$PROJECT_ROOT" "$DEFAULT_BACKUP_DIR")"
+  DEST_PARENT="$DEFAULT_BACKUP_DIR"
+  mkdir -p "$DEST_PARENT"
 fi
 
 TIMESTAMP="$(date +%Y%m%d_%H%M%S)"
@@ -241,7 +248,7 @@ generated_at="$(date --iso-8601=seconds)"
 dump_db(){
   local schema="$1" outfile="$2"
   echo "Dumping ${schema} -> ${outfile}"
-  docker exec ac-mysql mysqldump -uroot -p"$MYSQL_PW" "$schema" | gzip > "$outfile"
+  docker exec "$MYSQL_CONTAINER" mysqldump -uroot -p"$MYSQL_PW" "$schema" | gzip > "$outfile"
 }
 
 for db in "${ACTIVE_DBS[@]}"; do
diff --git a/scripts/bash/db-health-check.sh b/scripts/bash/db-health-check.sh
index 3f983b0..abc1276 100755
--- a/scripts/bash/db-health-check.sh
+++ b/scripts/bash/db-health-check.sh
@@ -32,6 +32,22 @@ SHOW_PENDING=0
 SHOW_MODULES=1
 CONTAINER_NAME="ac-mysql"
 
+resolve_path(){
+  local base="$1" path="$2"
+  if command -v python3 >/dev/null 2>&1; then
+    python3 - "$base" "$path" <<'PY'
+import os, sys
+base, path = sys.argv[1:3]
+if os.path.isabs(path):
+    print(os.path.normpath(path))
+else:
+    print(os.path.normpath(os.path.join(base, path)))
+PY
+  else
+    (cd "$base" && realpath -m "$path")
+  fi
+}
+
 usage() {
   cat <<'EOF'
 Usage: ./db-health-check.sh [options]
@@ -73,6 +89,10 @@ if [ -f "$PROJECT_ROOT/.env" ]; then
   set +a
 fi
 
+BACKUP_PATH_RAW="${BACKUP_PATH:-${STORAGE_PATH:-./storage}/backups}"
+BACKUP_PATH="$(resolve_path "$PROJECT_ROOT" "$BACKUP_PATH_RAW")"
+CONTAINER_NAME="${CONTAINER_MYSQL:-$CONTAINER_NAME}"
+
 MYSQL_HOST="${MYSQL_HOST:-ac-mysql}"
 MYSQL_PORT="${MYSQL_PORT:-3306}"
 MYSQL_USER="${MYSQL_USER:-root}"
@@ -263,7 +283,7 @@ show_module_updates() {
 
 # Get backup information
 get_backup_info() {
-  local backup_dir="$PROJECT_ROOT/storage/backups"
+  local backup_dir="$BACKUP_PATH"
 
   if [ ! -d "$backup_dir" ]; then
     printf "  ${ICON_INFO} No backups directory found\n"
diff --git a/scripts/bash/migrate-stack.sh b/scripts/bash/migrate-stack.sh
index 327be41..18f14b0 100755
--- a/scripts/bash/migrate-stack.sh
+++ b/scripts/bash/migrate-stack.sh
@@ -149,6 +149,7 @@ Options:
   --storage PATH        Remote storage directory (default: <project-dir>/storage)
   --skip-storage        Do not sync the storage directory
   --copy-source         Copy the full local project directory instead of syncing via git
+  --cleanup-runtime     Stop/remove existing ac-* containers and project images on remote
   --yes, -y             Auto-confirm prompts (for existing deployments)
   --help                Show this help
 EOF_HELP
@@ -164,6 +165,7 @@ REMOTE_STORAGE=""
 SKIP_STORAGE=0
 ASSUME_YES=0
 COPY_SOURCE=0
+CLEANUP_RUNTIME=0
 
 while [[ $# -gt 0 ]]; do
   case "$1" in
@@ -177,6 +179,7 @@ while [[ $# -gt 0 ]]; do
     --storage) REMOTE_STORAGE="$2"; shift 2;;
     --skip-storage) SKIP_STORAGE=1; shift;;
     --copy-source) COPY_SOURCE=1; shift;;
+    --cleanup-runtime) CLEANUP_RUNTIME=1; shift;;
     --yes|-y) ASSUME_YES=1; shift;;
     --help|-h) usage; exit 0;;
     *) echo "Unknown option: $1" >&2; usage; exit 1;;
@@ -385,6 +388,11 @@ setup_remote_repository(){
 }
 
 cleanup_stale_docker_resources(){
+  if [ "$CLEANUP_RUNTIME" -ne 1 ]; then
+    echo "⋅ Skipping remote runtime cleanup (containers and images preserved)."
+    return
+  fi
+
   echo "⋅ Cleaning up stale Docker resources on remote..."
 
   # Stop and remove old containers
diff --git a/scripts/bash/test-phase1-integration.sh b/scripts/bash/test-phase1-integration.sh
index 5ebb027..479b71a 100755
--- a/scripts/bash/test-phase1-integration.sh
+++ b/scripts/bash/test-phase1-integration.sh
@@ -22,6 +22,32 @@ ICON_ERROR="❌"
 ICON_INFO="ℹ️"
 ICON_TEST="🧪"
 
+resolve_path(){
+  local base="$1" path="$2"
+  if command -v python3 >/dev/null 2>&1; then
+    python3 - "$base" "$path" <<'PY'
+import os, sys
+base, path = sys.argv[1:3]
+if os.path.isabs(path):
+    print(os.path.normpath(path))
+else:
+    print(os.path.normpath(os.path.join(base, path)))
+PY
+  else
+    (cd "$base" && realpath -m "$path")
+  fi
+}
+
+if [ -f "$PROJECT_ROOT/.env" ]; then
+  set -a
+  # shellcheck disable=SC1091
+  source "$PROJECT_ROOT/.env"
+  set +a
+fi
+
+LOCAL_MODULES_DIR_RAW="${STORAGE_PATH_LOCAL:-./local-storage}/modules"
+LOCAL_MODULES_DIR="$(resolve_path "$PROJECT_ROOT" "$LOCAL_MODULES_DIR_RAW")"
+
 # Counters
 TESTS_TOTAL=0
 TESTS_PASSED=0
@@ -117,7 +143,7 @@ info "Running: python3 scripts/python/modules.py generate"
 if python3 scripts/python/modules.py \
     --env-path .env \
     --manifest config/module-manifest.json \
-    generate --output-dir local-storage/modules > /tmp/phase1-modules-generate.log 2>&1; then
+    generate --output-dir "$LOCAL_MODULES_DIR" > /tmp/phase1-modules-generate.log 2>&1; then
   ok "Module state generation successful"
 else
   # Check if it's just warnings
@@ -130,11 +156,11 @@ fi
 
 # Test 4: Verify SQL manifest created
 test_header "SQL Manifest Verification"
-if [ -f local-storage/modules/.sql-manifest.json ]; then
-  ok "SQL manifest created: local-storage/modules/.sql-manifest.json"
+if [ -f "$LOCAL_MODULES_DIR/.sql-manifest.json" ]; then
+  ok "SQL manifest created: $LOCAL_MODULES_DIR/.sql-manifest.json"
 
   # Check manifest structure
-  module_count=$(python3 -c "import json; data=json.load(open('local-storage/modules/.sql-manifest.json')); print(len(data.get('modules', [])))" 2>/dev/null || echo "0")
+  module_count=$(python3 -c "import json; data=json.load(open('$LOCAL_MODULES_DIR/.sql-manifest.json')); print(len(data.get('modules', [])))" 2>/dev/null || echo "0")
   info "Modules with SQL: $module_count"
 
   if [ "$module_count" -gt 0 ]; then
@@ -142,7 +168,7 @@ if [ -f local-storage/modules/.sql-manifest.json ]; then
 
     # Show first module
     info "Sample module SQL info:"
-    python3 -c "import json; data=json.load(open('local-storage/modules/.sql-manifest.json')); m=data['modules'][0] if data['modules'] else {}; print(f\"  Name: {m.get('name', 'N/A')}\n  SQL files: {len(m.get('sql_files', {}))}\") " 2>/dev/null || true
+    python3 -c "import json; data=json.load(open('$LOCAL_MODULES_DIR/.sql-manifest.json')); m=data['modules'][0] if data['modules'] else {}; print(f\"  Name: {m.get('name', 'N/A')}\n  SQL files: {len(m.get('sql_files', {}))}\") " 2>/dev/null || true
   else
     warn "No modules with SQL files (expected if modules not yet staged)"
   fi
@@ -152,19 +178,19 @@ fi
 
 # Test 5: Verify modules.env created
 test_header "Module Environment File Check"
-if [ -f local-storage/modules/modules.env ]; then
+if [ -f "$LOCAL_MODULES_DIR/modules.env" ]; then
   ok "modules.env created"
 
   # Check for key exports
-  if grep -q "MODULES_ENABLED=" local-storage/modules/modules.env; then
+  if grep -q "MODULES_ENABLED=" "$LOCAL_MODULES_DIR/modules.env"; then
     ok "MODULES_ENABLED variable present"
   fi
 
-  if grep -q "MODULES_REQUIRES_CUSTOM_BUILD=" local-storage/modules/modules.env; then
+  if grep -q "MODULES_REQUIRES_CUSTOM_BUILD=" "$LOCAL_MODULES_DIR/modules.env"; then
     ok "Build requirement flags present"
 
     # Check if build required
-    source local-storage/modules/modules.env
+    source "$LOCAL_MODULES_DIR/modules.env"
     if [ "${MODULES_REQUIRES_CUSTOM_BUILD:-0}" = "1" ]; then
       info "Custom build required (C++ modules enabled)"
     else
@@ -177,8 +203,8 @@ fi
 
 # Test 6: Check build requirement
 test_header "Build Requirement Check"
-if [ -f local-storage/modules/modules.env ]; then
-  source local-storage/modules/modules.env
+if [ -f "$LOCAL_MODULES_DIR/modules.env" ]; then
+  source "$LOCAL_MODULES_DIR/modules.env"
 
   info "MODULES_REQUIRES_CUSTOM_BUILD=${MODULES_REQUIRES_CUSTOM_BUILD:-0}"
   info "MODULES_REQUIRES_PLAYERBOT_SOURCE=${MODULES_REQUIRES_PLAYERBOT_SOURCE:-0}"
diff --git a/scripts/bash/verify-deployment.sh b/scripts/bash/verify-deployment.sh
index b84f825..05dca7d 100755
--- a/scripts/bash/verify-deployment.sh
+++ b/scripts/bash/verify-deployment.sh
@@ -98,12 +98,23 @@ read_env_value(){
   if [ -f "$env_path" ]; then
     value="$(grep -E "^${key}=" "$env_path" | tail -n1 | cut -d'=' -f2- | tr -d '\r')"
   fi
+  # Fallback to template defaults if not set in the chosen env file
+  if [ -z "$value" ] && [ -f "$TEMPLATE_FILE" ]; then
+    value="$(grep -E "^${key}=" "$TEMPLATE_FILE" | tail -n1 | cut -d'=' -f2- | tr -d '\r')"
+  fi
   if [ -z "$value" ]; then
     value="$default"
   fi
   echo "$value"
 }
 
+MYSQL_EXTERNAL_PORT="$(read_env_value MYSQL_EXTERNAL_PORT 64306)"
+AUTH_EXTERNAL_PORT="$(read_env_value AUTH_EXTERNAL_PORT 3784)"
+WORLD_EXTERNAL_PORT="$(read_env_value WORLD_EXTERNAL_PORT 8215)"
+SOAP_EXTERNAL_PORT="$(read_env_value SOAP_EXTERNAL_PORT 7778)"
+PMA_EXTERNAL_PORT="$(read_env_value PMA_EXTERNAL_PORT 8081)"
+KEIRA3_EXTERNAL_PORT="$(read_env_value KEIRA3_EXTERNAL_PORT 4201)"
+
 handle_auto_rebuild(){
   local storage_path
   storage_path="$(read_env_value STORAGE_PATH_LOCAL "./local-storage")"
@@ -171,7 +182,7 @@ health_checks(){
   check_health ac-worldserver || ((failures++))
   if [ "$QUICK" = false ]; then
     info "Port checks"
-    for port in 64306 3784 8215 7778 8081 4201; do
+    for port in "$MYSQL_EXTERNAL_PORT" "$AUTH_EXTERNAL_PORT" "$WORLD_EXTERNAL_PORT" "$SOAP_EXTERNAL_PORT" "$PMA_EXTERNAL_PORT" "$KEIRA3_EXTERNAL_PORT"; do
       if timeout 3 bash -c "</dev/tcp/127.0.0.1/$port" 2>/dev/null; then ok "port $port: open"; else warn "port $port: closed"; fi
     done
   fi
@@ -190,7 +201,7 @@ main(){
   fi
   health_checks
   handle_auto_rebuild
-  info "Endpoints: MySQL:64306, Auth:3784, World:8215, SOAP:7778, phpMyAdmin:8081, Keira3:4201"
+  info "Endpoints: MySQL:${MYSQL_EXTERNAL_PORT}, Auth:${AUTH_EXTERNAL_PORT}, World:${WORLD_EXTERNAL_PORT}, SOAP:${SOAP_EXTERNAL_PORT}, phpMyAdmin:${PMA_EXTERNAL_PORT}, Keira3:${KEIRA3_EXTERNAL_PORT}"
 }
 
 main "$@"