Bytor,
You need to look at the terms and conditions that were documented in the warranty statement. If you are still within the mileage and time requirements, then they should make good. I'd start at the dealer since they did the work and have the most to lose (a future sale). They should be willing to take up the issue with Chrysler for you. If not, then ask them why and get the number to call yourself.
I'm glad that they are covering the majority, but something still does not sound quite right. Why won't they cover the full repair if that is what the warranty stated? Also, from your post, it sounds like the transmission again needed to be rebuilt/replaced. What was the rot cause of the failure that they provided?
Good luck.
Bob