I finally got my Standalone LE2 swap to run. This is without and external LAN controlled modules.
A BIG thank you to the Internet person who suggested the Gen5 Vats disable fix.

If VATs disable is under the OS Tab then you have to do a "Write Entire".

Also go into Engine diagnostics and disable starter diagnostics.

Go to DTCs and do "NO ERROR reported" on every LAN communication error, all FPCM, all non High Pressure fuel errors, all starter circuit tests, and all TCM errors.
It might be easier to "No Error Report" everything and just add back the things you are worried about.

I may still have to reload the Automatic code with the Manual transmission code. We shall see.

Del Long