Jerking under any accelerating conditions?

Also changed TPS

Did you scan transmission or just engine?

I have this same problem and it is starting to really drive me nuts. I have recently replaced the EGR and TPS for other issues, the wires and plugs are about 3 years old and my Check Engine light comes on occasionally, but eventually goes off on its own. Engine temperature does not seem to be a factor and it will jerk when accelerating or at an even speed, but does not when at idle. I have seen that it could be one of the ignition coil packs, but how would one go about testing that theory?

After thinking about it I am guessing that you would check resistance, but how would that link to intermittent problems with spark problems?

I also realized you could use a little bit more info.
It is a 99 2.5L V6 Duratec standard transmission. The problem started directly after I replaced the TPS with a salvage yard replacement. Though it solved my idle problem I thought it being a very used and neglected part, it may be responsible in some way for the jerking (it actually feels like the engine is staling out for that half second so misfire does qualify) so I replaced it with a new TPS. It did not help. I have checked all the plug and wire connections and they are all solid, I have checked the EGR system for disconnected hoses and there are no codes as far as I know(every time I go to have it checked the CE Light is off). Previous to this I had it checked quite often since I was in school for Auto Tech and the only thing it was throwing were Oxygen Sensors which I had replaced.

That is all I can think of right now.

Cheers