Did you check the grounds and the ECU plug? At this point I would recommend swapping the ECU, and checking for leaks between the maf and throttle body. If unplugging the maf seems to make the problem worse, then it is probably not maf/leak related, but just to be sure.
Any pictures of the engine? Being that it was rebuilt have you checked compression?
and what do you mean jump. its automatic? So when it goes to shift, the rpm climbs up 2000rpm, then drops suddenly?
Sounds more and more electronic, wiring, grounds, computer. But the trans ecu is separate from the main ecu, so if the transmission is suddenly acting up AND the engine as well, clearly electrical / grounding needs to be checked. Did you ever check the alternator is putting out 14volts?
More and more I wonder about the mechanical aspect of your rebuilt engine. please get back about the compression results asap. Actually should have done that first, I thought you did but I dont see it on your check list.
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