What a suckpoo situation there Nathan. All that work and still have pay the dealer $$$. Now if the dealer had told you to begin with that the TCCM was bad rather than the encoder motor. Or maybe they both were bad at the beginning and they only looked as far as the encoder motor. Yep a messy situation. Hopefully once this is done all will be good for a while.
No ideal if it can be made to work. But it doesn't sound like an easy thing. It kind of depends on how the cooling is implemented. That is if it is stand alone in the seat or requires ducting from the main HVAC system.