The only reason you need aftermarket covers is for slightly more protection. I've seen a few stock ones get smashed in pretty good, but it takes a TON of effort to do it.
Definitely start with Rotors, and brake pads as well if they're worn. If your wheels are cupping, then you may also want to check your toe-in. Trail grapplers wear pretty evenly and for many miles.
I mainly carry bolts for my control arms and shocks/coilovers. They've been known to fall off if you don't check them regularly. A couple of extra lug nuts wouldn't hurt as well.
yeah, that makes a ton of sense. I have to assume wheel travel has the most effect on that. Can you recall what the total travel is front and rear? I can do 50/60 on the whoops now, and it's freakin' terrifying (which is probably a good thing).
If you can get the custom width you want I'd go that route. Getting the right scrub radius makes a bigger difference than people think. With the standard UD60s it seems like you have to push the wheel way out to clear everything.