Hey Everyone,
Thanks every much for your input. Disabling Scenery Folder 201 seems to cause a lot more issues as the airports in the surrounding areas and the elevation is all messed up (Likely due to the BGL file containing multiple airports/scenery).
I tried messing with it more, and found that a key issue when trying to use ADE to fix it, was that it wasn't compiling correctly. The Runway surface and some taxi link types were listed as 'blank' or '122' in ADE, these had to be corrected to Asphalt. Following that, I re-did the steps on Blaunarwal's guide, and this time it compiled correctly! With a CVX file as well, that helped resolve the terrain leveling issues nearby.
It was a really odd problem and I had no idea that something as obscure as runway surface type could cause this kind of issue. Hopefully this helps some folks facing similar issues! Thanks to everyone for pitching in.