I thought I would give an update.
Starting in 2006 with the ZF 6 speed transmission the transmission control module is located inside the transmission. Thats why I couldn't ever find it

I knew I wasn't totally crazy.
It turns out I was facing two problems with my X5 not starting.
The first was that when I removed/reinstalled the mechatronic I did not have the gear select lined up correctly which was the reason the car thought it was in gear and not Park or Neutral. The second was that the plug that goes in the sealing sleeve was faulty. The female sleeves in the plug were getting pushed further into the plug when I would go to install the plug instead of allowing the male ends to seat properly. This caused EGS errors the first time I turned the car on. I was pretty much doomed from that point on. The only way the car was going to be able to start was if the codes were cleared by BMW's computer. The Actron code reader I have couldn't pull those codes or clear them. There is a BMW internal TSB for this problem (see attachment). The annoying part is that this problem is really hard to find since the sleeves return to their normal position when you disconnect the plug! So unless you knew to check for that problem you would never find it.
So I had to have it towed to BMW. They fixed the transmission plug, cleared the egs codes, realigned the gear selector on the mechatronic and she was good to go. I am still quite pleased with the outcome though since I managed to complete most of the repairs on the list in my garage instead of paying someone to do them. Saved a ton of money and now the car runs and drives great.
Thanks for the help everyone!