GWS, Its hard for us to figure out what could have went wrong with your swap with no background info. Maybe if you post up the info on both the donor vehicle and the recipient we could help you out.

Year, trim model, build dates etc..

99 Gen 2.5, fixing blown head gasket
89 SWB- 33's, ARB Front locker, SR rear locker/axle, SR F brakes, winch, WST Offroad Armor all Around, 2.85 Aussie T-case Gears (SOLD)
Sold: (2) 95 SR's, 86 SWB, 90LWB, 91 LWB
-Can Change a timing belt in my sleep..