1. If it's a gear shifting issue while driving, especially a clunky downshift when braking at slow speeds, then a throttle cable adjustment is the first step. This is a very easy job described in the FSM at the beginning of the transmission section. This link by randy farnsworth tells you how to do it on the 442 from (93-94)
http://www.ih8mud.com/tech/80throttle.php but it is similar on the others. Make sure the cable receiver itself is properly aligned. This is a 1/4 banana job requiring a 12 mm wrench and 2 minutes that can make a surprising difference.
2. Next, check the tranny and transfer case fluids. top up, drain or flush the tranny fluid (using a low pressure flusher that uses the trucks own pump) and replace (you can use synthetic if you want). Top up or drain the gear oil in the transfer case (again synthetic can be used). This will probably not fix a bad clunk but its worth a try and good maintenance.