Welcome to the forum Komps02.
I've got to say, the number one best mod I have made to my two door JK is to remove the headrest from the rear seat. Now I can actually see something when I look in the rear view mirror. Number two best mod would be turning the seat belt warning chime off, so it doesn't continue to ding incessantly if I decide to drive my Jeep for a quarter of a mile off road without my seat belt on. Number three would be turning the TPMS sensors completely off with my Procal. That was just one more incessant ding that needed silenced. Now if I could just turn off all of the other electronic nanny crap that comes on new vehicles I would have it made.
Other than that, I think my best mod is a set of Dana 60 axles, with Eaton electric lockers and 4.56 gears, from Dynatrac. Then I would choose the Poison Spyder bumpers and rocker guards. I also need to mention the Teraflex 3" suspension. And the Warn winch is a great mod as well. And somewhere in here 35" Toyo MTs need to be mentioned.
2014 Wrangler Sport: Teraflex/Synergy 3" suspension lift, Fox 2.0 reservoir shocks, Tom Wood 1350 driveshafts, Dynatrac ProRock 60s w/ 4.56 gears and Eaton electric lockers, Warn front locking hubs, Currie Anti-rock front swaybar, Fox ATS, 37" Toyo MTs on 17x8.5 Vision Warlords, Poison Spyder bumpers and rocker guards, Warn M8000s winch, Teraflex tailgate hinge & spare tire carrier, Mopar head liner