You can re-gear a late model Trooper, but the options are limited. If you can find them, some late 1st generation Troopers came with 4.77 gears that can be swapped in, which will help you out a little, but not too much (I think stock is 4.60). For really big tires, even the 4.77's would probably be too high.
You can get Terra Low transfer case gears for 4-wheel low - those have great reviews, although there is a lot of labor involved to install them. Terra Low used to make diff gears for Troopers, but I think they stopped.
You can do ARB's front and rear, but in a Trooper with a rear Limited slip, you'd have to swap out the diff for an open one (ARB designed the locker for the open diff). There was supposed to be a Lockright diff being made for the rear, but I am not sure if that ever came about or not. You can always weld the rear end, too - but from what I have read and been told, a front ARB with the factory LSD in the read is pretty effective for most situations.
There are not lots of the fancy aftermarket stuff for Troopers, but most of the basic stuff is available - lift, lockers, HD suspension components. Scott can chime in with a lot more info, but you can check out
www.independent4x.com to see some of the stuff available.
Oops - sorry to sound like an Isuzu commercial - I think Toyota's are great, too!