Transmission Slipping after Changing Fluid

[Sciguy]

Hi all,
I have a problem that I am hoping you can help me solve before I go too far. I have made some modifications to my truck to help with performance like adding a Banks Power Pack to it. It is a 96 F-250. They moved the transmission cooler to accommodate the intercooler. When I started pulling with it after adding gauges even before I added the intercooler I notice that my Tranny temp would run up over 200 degrees. I decided to change out the transmission pan to a larger mag Hy-tech pan and switch to synthetic fluid. I then started a long trip and did not get but about 2 hours away from home when the temp on the transmission begin to climb again and this time it begin to have problems shifting and tripped a code on the computer and the o/d light begin to flash. I managed to limp back home and change trucks out but now I am concerned as to what to do.
The fluid I used was the Mobil 1 synthetic but the bottles were different colors but all of them said that they were for Ford Mercon fluid and some said Mercon/Mercon V.
I also have a SP diesel exhaust brake with T/C controller as well as the banks transcommand module attached to the transmission.
I am thinking that I need to drain all of the fluid back out and just replace it with regular fluid that is Mercon/Mercon V compatible.
Does this sound right to everyone or do I have problems with the transcommand module and the SP Diesel module? Or is it deeper transmission issues all the way around?
Please help...
Brian