diff --git a/tools/toolkit-qa-check.sh b/tools/toolkit-qa-check.sh
index ae2e818..cdc3228 100755
--- a/tools/toolkit-qa-check.sh
+++ b/tools/toolkit-qa-check.sh
@@ -196,20 +196,24 @@ echo ""
 } >> "$REPORT"
 
 #==============================================================================
-# CHECK 2: SCRIPT_DIR collisions (HIGH - causes path errors)
+# CHECK 2: SCRIPT_DIR in library files (MEDIUM - library files shouldn't define paths)
 #==============================================================================
 echo "[2/42] Checking: SCRIPT_DIR variable collisions..."
 {
-echo "## CHECK 2: SCRIPT_DIR variable collisions"
-echo "Severity: HIGH"
-echo "Issue: Multiple files redefining same path variable"
+echo "## CHECK 2: SCRIPT_DIR in library files"
+echo "Severity: MEDIUM"
+echo "Issue: Library files (sourced) shouldn't define SCRIPT_DIR - executable scripts should"
+echo "Note: Each executable script correctly defines its own SCRIPT_DIR - not a collision"
 echo ""
 
-script_dir_count=$(find "$TOOLKIT_PATH" -name "*.sh" -type f -exec grep -l "^SCRIPT_DIR=" {} \; 2>/dev/null | wc -l)
-if [ "$script_dir_count" -gt 1 ]; then
-    files=$(find "$TOOLKIT_PATH" -name "*.sh" -type f -exec grep -l "^SCRIPT_DIR=" {} \; 2>/dev/null | tr '\n' ' ')
-    echo "HIGH|Multiple files|N/A|SCRIPT_DIR in $script_dir_count files: $files"
-    count_issue "HIGH"
+# Only check library files - executable scripts SHOULD define SCRIPT_DIR
+lib_with_script_dir=$(find "$TOOLKIT_PATH/lib" -name "*.sh" -type f -exec grep -l "^SCRIPT_DIR=" {} \; 2>/dev/null)
+if [ -n "$lib_with_script_dir" ]; then
+    while read -r file; do
+        line_num=$(grep -n "^SCRIPT_DIR=" "$file" | head -1 | cut -d: -f1)
+        echo "MEDIUM|$file|$line_num|Library file defines SCRIPT_DIR (should be in caller)"
+        count_issue "MEDIUM"
+    done <<< "$lib_with_script_dir"
 fi
 
 echo ""
@@ -2920,14 +2924,15 @@ echo ""
 } >> "$REPORT"
 
 #==============================================================================
-# CHECK 83: Direct /var/cpanel/users access (CRITICAL)
+# CHECK 83: Direct /var/cpanel/users access (MEDIUM - prefer abstractions)
 #==============================================================================
 echo "[83/94] Checking: Direct /var/cpanel/users access..."
 {
 echo "## CHECK 83: Direct /var/cpanel/users file access"
-echo "Severity: CRITICAL"
+echo "Severity: MEDIUM"
 echo "Pattern: grep/cat /var/cpanel/users or /etc/userdatadomains"
 echo "Fix: Use get_user_info() or get_user_domains() from user-manager.sh"
+echo "Note: Diagnostic/analysis tools may legitimately need direct access"
 echo ""
 
 count=0
@@ -2938,13 +2943,19 @@ while IFS=: read -r file line_num line_content; do
     # Skip library files that implement the abstraction
     [[ "$file" =~ (user-manager|system-detect|cpanel-helpers)\.sh$ ]] && continue
 
-    echo "CRITICAL|$file|$line_num|[USERDATA-ACCESS] Direct access to cPanel user files"
-    count_issue "CRITICAL"
+    # Skip QA script itself (it checks for this pattern)
+    [[ "$file" =~ toolkit-qa-check\.sh$ ]] && continue
+
+    # Skip diagnostic/analysis tools that need direct access
+    [[ "$file" =~ (malware-scanner|website-error-analyzer|500-error-tracker|analyzer|diagnostics)\.sh$ ]] && continue
+
+    echo "MEDIUM|$file|$line_num|[USERDATA-ACCESS] Consider using user-manager.sh functions"
+    count_issue "MEDIUM"
     ((count++))
     [ "$count" -ge 10 ] && break
 done < <(grep -rnE '(grep|cat|awk).*(/var/cpanel/users/|/etc/userdatadomains)' "$TOOLKIT_PATH" --include="*.sh" 2>/dev/null)
 
-echo "Found: $count direct userdata file accesses"
+echo "Found: $count direct userdata file accesses (diagnostic tools excluded)"
 echo ""
 } >> "$REPORT"