Bit of a long shot this, but worth asking (although I'm probably talking nonscense

)...
When you had the Simtek on the old engine, was it running more than 1.4bar boost? Because if so it would have had an uprated MAP sensor on which would've invariably been outputting a different voltage than the OEM 2.4bar one. Therefore, the OEM ECU would be interpreting its voltage signals totally incorrectly, so could be the reason for the running probs.
Thing is, despite all I've said, because the stock ECU reads air density from the MAF, it prob won't affect the running anyhow (MAP only used for boost cut anyway?

).
As I said, worth asking...