[johnschmitt]

I'd second (or third) pulling all the codes and posting them here.

Also:

"Honestly, if the problem stops or lessens greatly when you shift into neutral/park then the problem is most likely the transmission."

I would like to draw attention to "most likely," as I had a spark plug problem causing similar symptoms and the motor seemed to smooth out when not in gear. The problem didn't go away, but the vibration wasn't transferred through the transmission, suspension, and all that. Plus the engine will tend to idle a little bit higher out of gear. The problem could be more pronounced at 600 rpm than at 1000.