Hey Jonathon. With the old motor, I'm thinking that you have bad compression rings, as well as a probable bad CKP (Crank Position Sensor). What I would do, if you're replacing the engine, is actually pretty simple--just change the lower end (meaning block, crank, pistons, rods, main bearings, oil pump). I would put your old oil pan on the donor block, to retain your oil level sensor position; I would also change out the old head to the donor block, that way you don't lose your sensors (you probably have a cam sensor, I'm thinking). Also, I would also, before you put it in, check the resistance on the CKP and change it out, if it needs to be. There shouldn't be any issues, in terms of the timing system; change out and check your water pump from the old engine and reuse it, if you can. I would also reuse both the intake and exhaust manifolds, as well as the throttle body from the old engine. As most of what you are pulling is OBD-II, like you said, you should only have to change out the block and transfer everything from the old block to the new. If you do things that way, it should save you headache, and most importantly, time.
