[Iflylow]

Thanks for that info-I have the 3.4, so I'm obviously not familiar with the 2.4.

Do you have a tach? Maybe the miss only occurs in a certain RPM band, and driving in 3rd gear versus overdrive puts you in that RPM band?

Or, as you suggest, maybe it isn't really an ignition related miss, but a transmission slip or buck. I know on the 3.4, if there is an ignition related misfire, a code will be set if it continues long enough (a few seconds in my experience).
Xeroinfinity knows a lot about these transmissions. Send him a message, he'll probably know what's up.