I would get a 2.0 ECU and piggy back it. Since after more modificaion, piggyback is necessary to modify the mapping. And also piggyback can modify the ignition timing, and fuel duty cycle. Can maximise the potential of the hardware. Futhermore, piggyback is transferable to next car, so its worth the investment.
Its interesting if the pinouts at the harness connected to ECU is identical to 2.0 ECU. It means the ECU is same brand and same type, only fuel mapping is different due to cc difference. Which I highly doubt so. I think need to cut and rewire the wires to new ECU.
I am surprise flywheel do not fit. I thought all GM 6 bolt flywheel is the same, only port type or flat type. But 6 bolts are the same. Pls ask your mechanic to turn the flywheel, because the 6 bolts is not equi-distance to each other. 2 bolts are nearest to each other and two bolts are furtherest to each other. Which naked eye cannot spot it. Turn the flywheel around in cycle. It should fit. There is only 4 tpe of flywheel, 6 bolt pot, 6 bolt flat, 8 bot pot, 8 bolt flat GM flywheel. So as long as 6 bolt, it should be fine. In fact I am using 6 bolt Pot flywheel from Opel. Same from GM, it fits also.