Car most likely needs a crank relearn, performed with a Tech 2 at your local friendly money-loving dealership.
I've done 10-15 GM engine swaps with no mishap, about 5 were 3400s, but I did have one that ran fine for 5 minutes, then bogging down. Only fixed was a crank relearn. (First the dealership sold me a MAF, but I made them take it back when it didn't fix the problem -I was selling the car anyways)
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