besides them pulling codes have you or anyone does any diagnostic on it? like basic misfire stuff? I don't know forsure, but I would expect the Stabilitrak fault codes to be non P codes.
was the old engine tapping badly for 2 cyl to be down from afm, it should have been tapping pretty hard.
you also didn't say if you had the ecm tuned to disable the afm since the new engine doesn't have it and you probably need or at least could use a tune for the cam that's in it.
if you still have the old engine laying around, having your guy pull the valve covers off and turn the engine over while looking for loose rockers from stuck valves might help you know which direction to go with troubles shooting.
on a side note, the shop isn't 100% wrong, usually buying a rebuilt or built engine used from someone you don't know and then not inspecting it really well doesn't turn out great. so hard to say, you're going to need to go back and do all the diagnostics you'd have done to the first engine and then go. from there