i run a k&n filter in my stock air box. that was a good upgrade in my eyes. i run ahelix ptpt throttle body spacer. it helps i get better mileage & the engine spools up faster. if you can only fit 31's it may only be a 3" lift. when you do your cooling flush you may want to pull your t-stat, i did & i drilled a little hole ( 5/16 ) in it, that allowed the air to burp out fully, it doesnt hurt anything. 3.55 gears are ok as long as you dont try to tow a trailer or pull anything bigger than you out of the mud. 373's or 410's are the way to go.
do you have a reese hitch on the back? get one if not. best thing to pull with & get the recovery hook package for the xj for the front. the cherokees lack hard points to pull from.