Update: it is currently at the dealer. To answer your questions above - it is a 4 button system and yes, I did have the battery un-hooked when doing the repair. I also left it un-hooked overnight hoping that the code would clear.
I took it to the dealer because I think it is the TCCM. They have done some prelim tests on the electrical system and the current code is:
-C0324 T-Case Lock Circuit High.
They are telling me that either the TCCM is bad or there is a short in the wiring between the TCCM and the encoder motor. I don't really understand all of the electrical stuff so I am leaving it to them. They are tearing into it as I type in order to further test it to see exactly what is wrong. Surprising, they were willing to print out a whole bunch of wiring diagrams to give to me and tell me which specific wires to test out and then they were even going to tell me how to tell what the specific problem was so that I could do it myself.
If it ends up being the TCCM it will be $800 for the repair - $500 for the part and $300 for labor. As for the encoder motor that I already replaced, he told me that there are not any codes currently showing that there is a problem with that motor. It was a different dealer that told me that yesterday - and they are thinking that maybe the computer / wiring problems fried the old encoder. Who knows. If it is the TCCM...this entire ordeal will have costed me about $1,100. New dash switch, new encoder motor, and new TCCM. What a nightmare.
I am hoping they just fix it - I don't really have the time or patience anymore to keep throwing parts at it, and I don't think I can get a TCCM from my local auto parts store.
Thanks again for all of the help!