Your Couatl.INI file is messed up, you haven't placed each command on a new line as they should, and you have a duplicate logFile line so, first fix that.
1.anytime I would click a gate to warp to it would warp me to some random spot at the airport that wasn't a gate and was just between a runway and a taxiway.
This is caused by the wrong scenery loaded, usually due to confling sceneries, which can be checked by opening the scenery customization page.
3. I was wondering if you can configure the addon scenery to read the "C:\Program Files (x86)\Steam\steamapps\common\FSX\Addon Scenery" and all the folders in there.
There's nothing to configure. GSX will use every Scenery Area listed in the Scenery.CFG file
2. I click rebuild cache and it comes up with regeneration failure. I have seen people say to delete the files.bin in the programdata and it only works for a short period of time before something else goes wrong. (zip file is above for any of these)
That error is either caused by the antivirus, or by having started the sim too quickly after closing a previous session, resulting in file locks from the previous session not being cleared by Windows. Try after a Windows restart.