The over heating problem has nothing to do with it being a 3.0, the wrong t-stat didn't help it any. I had a similar overheating problem, though it only occurred after using the A/C in 100+ heat, and after the first time I started replacing/checking the usual suspects, i.e., coolant, T-stat, cleaned the Rad fins etc. After the 2nd time I poulled tha rad and had it rebuilt, that solved the problem. If you get it running again, run your hand along the rad, and check for cool/warm spots, you could have a clogged radiator.
Chances are though the repeat over heating stressed the gasket and possibly warped the heads. Did you keep any of the old 3.0, didn't it obly have a burnt valve. You might also talk to the guy you got the engine from and see if he is willing to return some of your money since he put the wrong t-stat in it.
Grumpy1
If Blackdog doesn't want the diesel, what are you wanting for it. I have a buddy that has been looking for one for his '91 trail rig.