Make sure that you've got the right cables plugged in to the right spots. the cables and connectors are identical for the MAF and the throttle body with the exception that one has 6 wires and the other as 5. I did this when I first started the car up and had the same issue.
Also, rev 1 and 2 of my tunes were pretty jerky, so a revised tune might clear that up.
I've noticed that my car has been a little jerkier lately since that arctic front came through, so maybe that has some play in it
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