Make sure you use a 91-97 donor for the tranny, otherwise, it shouldn't be a big issue at all to swap.
Some of those years may require minor wiring splicing, nothing more than a few butt splices and a crimper is required, along with not being color blind.
98 and later donor you'll need to swap your 4x4 adapter housing, output speed sensor, and output speed sensor drive rotor over. Not that hard, just annoying.
I would run it till it stops moving, AW4s are pretty darn bulletproof. Also adjust your throttle valve cable and make sure the fluid is full and clean... if it's a quart or so low, it'll sometimes bang into gear after a hard stop and/or slip into second when shifting for the first time after being started cold.