A lot of the issues you may be running up against revolves around the technicians trained (or not so much) to repair the Crossfires. So, it actually may not be the Crossfire itself. Not too many reports of the ECU going bad seem to be located here, so it could be a combination of effects, which would take some time to fix (which it has). Being a rather sophisticated vehicle even though it's built on an older platform, you might (if the current dealership can't) try taking it elsewhere... With 2 simultaneous issues, the symptoms should at least change... (either the ECU or the transmission). But first find a shop/dealership that will do warranty work on the Xfire, and get some references of past Xfire customers that were there if they will release names/numbers. The dealership where we bought our Xfire has only ONE technician that is trained on the Xfire. Luckily, he must have been paying attention in class... It still took a long time to get the right parts (from Germany, and large parts distribution centers are only located in a couple of places in the States that may stockpile the part). But, they did do a good job and fix it right the first time. And this was just the E-19 recall for the fan control module and some paint touch up from plastic that had melted on the kick panel (sitting on the lot with plastic for 400 days is not good for the plastic kick panel).
It's certainly not fun to be without your car for an extended time, and at least it's under warranty still... If you still go for the lemon filing, make sure to get plenty of documentation on the fixes... The Chrysler folks may just decide to blame the person who worked on your car. Going to 2 separate dealerships replacing parts with no resolve may eliminate the "technician" side of the story and really get to the meat of the matter, the car and /or parts themselves.