Help Dropping in a "new" motor and Tranny

I picked up a low mileage 1998 4.0 and AW4 tranny this weekend. I plan on using them to replace my "hole in the piston" 4.0 and AW4 with 150k miles on it. What do I need to do/check if anything to the AW4 before swapping it into the jeep and is there anything you would do to the 4.0 before dropping it in ie new rear main seal etc. It does have a crack in the exhaust manifold where it bolts up to the down tube and I was planning on welding that closed. Any and all ideas / comments or shared experiences are greatly appreciated. Hopefully this will get me back on the trail. Special thanks to Wren from this site on the deal on the motor and tranny. OOOOPs forgot to post my Jeep is a 1996 Cherokee

Ok what year is your jeep??

Motor: New oil pump, rear main seal, pan gasket....since you have it out.
Tranny: nothing really

Make sure the flex plate is the one you need for your jeep...As you didn't list a year. my jeep has a renix system and I had to change out the flex plate so the CPS would read the right signal.

1996 thanks I edited my post

Anyone have pictures of a non-HO and HO flex plate??

I have one of each and need to figure out which will work on my renix CPS 1990.

Thanks.

i allways like to tear em apart and go through everything and replace all the seals espically the tougher ones that would piss me off later. and liek someone said allready oil pump while your there. it may be worth it later.