diff --git a/scripts/security-fuzz.sh b/scripts/security-fuzz.sh
index a396f609f..52ed25c54 100755
--- a/scripts/security-fuzz.sh
+++ b/scripts/security-fuzz.sh
@@ -91,7 +91,7 @@ test_invalid_index_interactive() {
     HOME="$FUZZ_HOME" CBM_CACHE_DIR="$FUZZ_CACHE" \
         python3 "$(dirname "$0")/test_mcp_interactive.py" "$BINARY" \
         --scenario invalid-index --repo-path /nonexistent/path/abc123 \
-        --response-timeout 30 --exit-timeout 15 > "$tmpoutput" 2>&1 || ec=$?
+        --response-timeout 45 --exit-timeout 15 > "$tmpoutput" 2>&1 || ec=$?
 
     if [[ $ec -eq 0 ]]; then
         PASS=$((PASS + 1))
diff --git a/scripts/smoke-test.sh b/scripts/smoke-test.sh
index 04e6225f5..be84d1fbc 100755
--- a/scripts/smoke-test.sh
+++ b/scripts/smoke-test.sh
@@ -564,7 +564,7 @@ echo "=== Phase 4: security checks ==="
 echo "Testing clean shutdown..."
 if ! python3 "$REPO_ROOT/scripts/test_mcp_interactive.py" \
     "$BINARY" --scenario initialize --repo-path "$TMPDIR" \
-    --response-timeout 30 --exit-timeout 8 > /dev/null; then
+    --response-timeout 45 --exit-timeout 8 > /dev/null; then
   echo "FAIL: initialized binary did not exit within 8 seconds after EOF"
   exit 1
 fi
@@ -601,7 +601,7 @@ echo "=== Phase 5: MCP stdio transport (agent handshake) ==="
 
 # Helper: run binary in background with input, wait up to N seconds, collect output
 mcp_run() {
-  local input_file="$1" output_file="$2" max_wait="${3:-10}"
+  local input_file="$1" output_file="$2" max_wait="${3:-45}"
   "$BINARY" < "$input_file" > "$output_file" 2>/dev/null &
   local pid=$!
   local waited=0
@@ -621,7 +621,7 @@ cat > "$MCP_INPUT" << 'MCPEOF'
 {"jsonrpc":"2.0","id":2,"method":"tools/list","params":{}}
 MCPEOF
 
-mcp_run "$MCP_INPUT" "$MCP_OUTPUT" 10
+mcp_run "$MCP_INPUT" "$MCP_OUTPUT" 45
 
 # 5a: Verify initialize response (id:1)
 if ! grep -q '"id":1' "$MCP_OUTPUT"; then
@@ -706,7 +706,7 @@ TOOLS_MSG='{"jsonrpc":"2.0","id":2,"method":"tools/list","params":{}}'
 TOOLS_LEN=${#TOOLS_MSG}
 printf "Content-Length: %d\r\n\r\n%s" "$TOOLS_LEN" "$TOOLS_MSG" >> "$MCP_CL_INPUT"
 
-mcp_run "$MCP_CL_INPUT" "$MCP_CL_OUTPUT" 10
+mcp_run "$MCP_CL_INPUT" "$MCP_CL_OUTPUT" 45
 
 if ! grep -q '"id":1' "$MCP_CL_OUTPUT" || ! grep -q '"id":2' "$MCP_CL_OUTPUT"; then
   echo "FAIL: Content-Length framed handshake did not produce both responses"
@@ -3154,7 +3154,7 @@ echo "=== Phase 16: stdio server leaves no orphan after shutdown ==="
 "$BINARY" < /dev/null > /dev/null 2>&1 &
 SHUT_SRV_PID=$!
 SHUT_GONE=0
-for _ in $(seq 1 60); do            # bounded ~6s wait (60 × 0.1s)
+for _ in $(seq 1 400); do           # bounded ~40s wait (400 × 0.1s)
   if ! kill -0 "$SHUT_SRV_PID" 2>/dev/null; then SHUT_GONE=1; break; fi
   sleep 0.1
 done
diff --git a/scripts/test_mcp_interactive.py b/scripts/test_mcp_interactive.py
index 5421bd514..4db2a902c 100644
--- a/scripts/test_mcp_interactive.py
+++ b/scripts/test_mcp_interactive.py
@@ -271,7 +271,7 @@ def main() -> int:
         required=True,
     )
     parser.add_argument("--repo-path", required=True)
-    parser.add_argument("--response-timeout", type=float, default=30.0)
+    parser.add_argument("--response-timeout", type=float, default=45.0)
     parser.add_argument("--exit-timeout", type=float, default=15.0)
     args = parser.parse_args()
 
diff --git a/src/cli/cli.c b/src/cli/cli.c
index 4d2364a4e..7641a1228 100644
--- a/src/cli/cli.c
+++ b/src/cli/cli.c
@@ -1191,6 +1191,7 @@ void cbm_cli_set_activation_cleanup_failure_for_test(bool enabled);
 int cbm_cli_activation_abort_cleanup_probe_for_test(void);
 #endif
 
+#if !defined(_WIN32) || defined(CBM_CLI_ENABLE_TEST_API)
 static void cli_activation_transaction_abort_or_fail_stop(
     cbm_activation_transaction_t **transaction_io, const char *component) {
     int cleanup_status = cli_activation_transaction_abort(transaction_io);
@@ -1204,6 +1205,7 @@ static void cli_activation_transaction_abort_or_fail_stop(
                                          component ? component : "activation_transaction_cleanup");
     }
 }
+#endif
 
 #ifdef CBM_CLI_ENABLE_TEST_API
 void cbm_cli_set_activation_cleanup_failure_for_test(bool enabled) {
diff --git a/src/main.c b/src/main.c
index 0c5dd7cab..d76546993 100644
--- a/src/main.c
+++ b/src/main.c
@@ -37,6 +37,7 @@ enum {
     MAIN_PATH_CAP = 4096,
     MAIN_CONNECT_TIMEOUT_MS = 1000,
     MAIN_STARTUP_TIMEOUT_MS = 10000,
+    MAIN_MCP_STARTUP_TIMEOUT_MS = 30000,
     MAIN_REQUEST_TIMEOUT_MS = 24 * 60 * 60 * 1000,
     MAIN_HOOK_CONNECT_TIMEOUT_MS = 250,
     MAIN_HOOK_STARTUP_TIMEOUT_MS = 1500,
@@ -1631,7 +1632,7 @@ int main(int argc, char **argv) {
             ? cbm_version_cohort_acquire(client_cohort_manager, &identity,
                                          main_deadline_after(role == CBM_DAEMON_PROCESS_HOOK_CLIENT
                                                                  ? MAIN_HOOK_STARTUP_TIMEOUT_MS
-                                                                 : MAIN_STARTUP_TIMEOUT_MS),
+                                                                 : MAIN_MCP_STARTUP_TIMEOUT_MS),
                                          &client_cohort_lease, &client_cohort_conflict)
             : CBM_VERSION_COHORT_IO;
     if (client_cohort_status != CBM_VERSION_COHORT_OK) {
@@ -1657,7 +1658,7 @@ int main(int argc, char **argv) {
         .connect_timeout_ms = role == CBM_DAEMON_PROCESS_HOOK_CLIENT ? MAIN_HOOK_CONNECT_TIMEOUT_MS
                                                                      : MAIN_CONNECT_TIMEOUT_MS,
         .startup_timeout_ms = role == CBM_DAEMON_PROCESS_HOOK_CLIENT ? MAIN_HOOK_STARTUP_TIMEOUT_MS
-                                                                     : MAIN_STARTUP_TIMEOUT_MS,
+                                                                     : MAIN_MCP_STARTUP_TIMEOUT_MS,
     };
     cbm_daemon_bootstrap_result_t bootstrap_result;
     cbm_daemon_bootstrap_status_t bootstrap_status =