so how do I go about fixing the mesh conflicts?
I never said you have a mesh conflict at JFK. You said you have "hills on the runway" at TNCM, so I've replied THAT one is a mesh conflict.
It is a fresh install of FSX. The airports have the original taxiway lines and then FSDreamteam taxi lines so the lights and all are off.
This, instead, it's an AFCAD conflict, caused by another scenery, which should be fixed by looking for the duplicate AFCAD with the free FSX airport scanner program. You said it didn't find any, I've replied that sometimes AFCAD in conflict might not be found, and they usually come with AI Traffic package products, so you must remove them manually.
Of course, this assuming you haven't played with the Scenery Library order: JFK V2 should be on top of the Scenery Library (or, at least, on top of everything else that might cause a conflict with it), which is where the installer puts it by default.