I have the rough idle on my SE 5-speed manual. Does it when the engine is nice and warm. Dealer swapped the throttle body but the issue persists. I tried different gas, premium...
All I can say is that it is not normal. Should not shake like that at idle, especially with no load against the engine as with an auto in drive and stopped with the brakes.
I may try to pull the connector to the MAF to see what it does.