Very strange Dan, I had the exact same symptoms of ~2000rpm miss on a 4A with a Microtech, ended up being an ECU issue and had to go back. When returned it worked fine.
Yours is odd though that it was fine on the previous engine and now is an issue.
If the crank and cam sensors come up fine in testing I'd point the finger at the ECU, even though it doesn't make a great deal of sense.
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