I'm a little confused in what you are saying the problem is. Is the engine itself running rough or is it that it shutters when you press the gas after a complete stop, having a pause where the engine revs then suddenly it jerks and moves?
If the engine itself is running rough, then I would recommend talking to people who have had 3.5Ls and asking them if they have ever encountered this before. I would go to our sister forum
www.dodgeforum.com and ask as well over there. When doing this, you might want to ask in the 2nd generation Intrepid section as a 3.5L V6 question since these owners have had these models for a longer time and might have already experienced many of these issues. There are a few regulars over there who are very useful in that section.
If it is the second, then the problem is probably simple. The check engine light is likely crying wolf, while the transmission is trying to shift back down to first and hasn't had the time to get it done yet before you press the gas. This is a typical problem with Chrysler automatics and fortunately extremely easy to fix. Just use the gear shifter to shift it into "L" around 10mph, will force it to go into first and it will be ready to take off.
challygirl, I'm not sure how relevant the problem with the R/T's torque converters would be since the R/T and the SE have completely different transmissions. The SE has a Chrysler 42RLE, the R/T has a Mercedes W5A580.