I have adjusted my mesh resolution to 5m and my complexity is at 100. I deleted the AES Basepack and AFD.
Again, you are trying to fix it in the fast way, by disabling or removing whole areas of what can be undoubtedly identified as a 3rd party product. But if something has placed a .BGL containing a mesh in one of the default folders, you must hunt that specific .BGL.
Should I just do a clean install?
It's either that, or the search for the stray .BGL. Or perhaps a *missing* .BGL from a default install, that a clean install will surely fix.
.I ran the FST Scenery tool which supposedly fixes a troublesome scenery.cfg. Is there anything else I should try before going for a reinstall
No idea what that tool is, but if it just fixes a scenery.cfg with errors, it won't help with a conflicting or missing .BGL so, unless you know how to find it, a clean reinstall might be your only option.
Unfortunately, there's no such thing like the free FSX Airport Scanner tool (that helps finding conflicting AFCADs) for meshes.