Welcome Josh- Lots of info and experience here to help you fix it all up.
Here's some references for you to get you started on your list.

~EDIT: I also need to get my ABS light and BRAKE light off somehow
http://vehicross.info/forums/showpos...5&postcount=13
http://vehicross.info/forums/showpos...4&postcount=12


6. Gatorback info.....should be low on your priority list IMHO
http://vehicross.info/forums/showthr...gatorback+mike

http://vehicross.info/forums/showthr...gatorback+mike

http://vehicross.info/forums/showthr...gatorback+mike

Extensive info on "cladding", here's just one long thread:
http://vehicross.info/forums/showthr...gatorback+mike


7. Heres the fun part, the IDIOT slammed the VX into 4 LOW on the interstate so the mechanic removed part of the driveshaft that powers the front wheel drive. I have the part, its as long as my arm and its in the back seat. Who even knows whats broken?
http://vehicross.info/forums/showpos...7&postcount=11


8. Replace headlight gaskets, which he removed when he added LED rings to the headlights.
These aren't "necessary"...I ran for almost 2 yrs w/o them, no problems. Can order new ones through "Merlin". He's our parts guru!
Merlin
St. Charles Isuzu
MISSOURI
(800) 727-8066
Mention the forum to get discount & free shipping.


9. Replace the fog lights because his are too big, almost burned out and stuck in there with freakin chewing gum (WTF)
ASSUMING you're talking about the front round marker lights in front bumper:
http://vehicross.info/forums/showpos...38&postcount=8


11. Replace back, interior spare tire cover...because its GONE!
13. Replace back tire cover on door where he cut a hole for his back up camera OMG! (Are you talking about the exterior part of the rear tailgate here?)
Not sure but "bob barker" may still have the interior back door cover available.
http://vehicross.info/forums/showthr...hlight=muffler


14. Repair both windows.
This post is way too long but has a ton of threads regarding this, but you can keep it for reference.
http://www.vehicross.info/forums/sho...92&postcount=3



Good luck and remember there's a ton of really smart peeps here that can help you on this stuff!