Justin, I see you called. Ill try to get a call back to you tonight. Trying to finish some stuff up here.
Try this...
When you try to start truck and it shuts down, the security light will light up on the dash. This is telling you VATS has been enabled. This is common when switching out controlers, or sometimes letting the truck sit without battery power for long periods of time. Follow the instruction to do the VATS relearn process.
Try to start it, then turn the key back to run. DO NOT TURN IT TO OFF.
Wait 11 minutes (time it).
Try to start again, then turn key back to run.
Wait 11 minutes (time it).
On the third cycle, it will ignore the VIN differences in the various modules and will start.
A Tech2 can be used to do this instead waiting time.