I don't have enough knowledge about running TMCC engines in conventional mode to be of much help. However, I have seen this set being run in a TMCC environment, and the operator wasn't having any problems with it. Lionel did these 3-engine sets in B&M, Wabash, and Florida East Coast liveries. Maybe there were some issues, but I've never heard any reports of this.
The reverse pulling you have must be quite severe to strip gears like that. I have quite a few of these Lionel Geeps from the same era, and they've been pretty bulletproof. I've put lots of miles on them without any problems, and have never had to replace any gears. I have also run two powered units together back-to-back in TMCC and Legacy environments, and have had no problems.
For whatever reason, running your two TMCC engines back-to-back in conventional mode is creating gear problems, and it sounds like you've had other control issues as well. With all the money you've spent on repairs, you could have picked up a basic TMCC setup in the used market for far less, and be running the engines the way they were designed. My guess is that your problems would be solved, and you'd be having a lot more fun running them with TMCC, too.
