We just added a Super Admin window inside of your GHL where you can troubleshoot and inspect your current Toolkit Set Up.
You can find the Toolkit SuperAdmin in your User Menu (top-right avatar in GHL).
I do a full walk through in the video, but at a glance you can tell:
Is everything installed correctly?
Which location group is the sub account in and why?
Why isn't a menu item showing up? Is it native GHL or the Toolkit?
What snapshots are connected to this sub account?
Additionally, you can disable the Customizer, and CSS to do more investigation on your own.