wow, that's a lot of issues! It's going to be hard to pinpoint any one thing, but I can get the ball rolling a bit. What year jeep did your new motor come out of? There can be differences with the computers that could be causing some of this stuff. The loss of power and not shifting at the right time is leading me towards your catalytic converter being clogged. Mudderoy was having some of those issues caused by that. Being hard to start, hmm... when was your fuel filter/pump assembly last changed? It's no fun because you have to drop the gas tank Timing could also be off, the motor could also have issues... was it compression tested at the shop?