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Stupid question: Is the 1999 engine you swapped in a T7 or a T5 (since both variants were still produced in 1999)? I ask because your car is a 1997 so it started life as a T5 for sure. So, if you in fact swapped in a T7 engine, did you also swap in the T7 ECU and harness? I would assume yes as I don't know that the car would even run otherwise. On the other hand, maybe that is why it is stuck on base boost - maybe it is in limp home mode due an identity crisis (i.e. the ECU is extremely confused).
