2003 Ford F350 Transmission problems after computer tune up

Transmission problem
2003 Ford F350 V8 Four Wheel Drive Automatic

I have a 03' F-350 with the 6.0L and an automatic. I use a SCT programer. Inovative Diesel sells me the custom tunes, they are the best. I updated the firmware on my programer through SCT, They did the updating. Then I tried to reprogram my truck. On the stock tune it would barely start. I then put a custom tune. The transmition would not fully engauge in revrese, not shift above 4th gear, and would act like it was in netural while driving sometimes. I called Inovative Diesel, explained the porblems that I have, they sent me new updated custom tunes. When I installed one the engine starts and runs great but the transmition still has the same problems, light on the tow mode button flashes also. They told me to take it in and have ford to reset the computer. They told me that I now have 2 injectors bad and the plantary is out of the transmission. I told them to reset the computer, 10min later they told me the computer was reflashed and it did no good, I drove the truck home. These problems started the minute I tried to reprogram the truck. Help me please. Chuck