So here is what I believe are my next steps, please double check my logic.
Before I pulled the 06 apart, I used the V2 and read off the ECM stock tune. Having said that, This is how I believe I need to proceed.
1. Send stock tune from 06 to ATP trucks to have the EGR deleted, switched to single fuel tank config and flip the polarity for the LB7 fuel level sending unit. I also will purchase a DSP 5 from them, with their corresponding level 1 tuning. (I am not wed to ATP, they just seem to get high recommendations. If someone like Russ, can do this tuning I would certainly use him or one of the other members who have helped with these conversions. Ben is just too busy, though.)
2. Do EGR delete and PVC reroute on the LBZ, while it is sitting on the garage floor. (possibly replace #8 glow plug as well, donor truck was throwing a MIL on that)
3. Pull the T case and 5 speed alli out of the 03.
4. Stand the (5) and (6) speeds on the bellhousings next to each other. Then convert the (6) speed, to 4wd, using the tailhousing and output shaft from the (5) speed.
5. Reinstall (6) speed and T case back in the 03.
6. Remove the 03 from the lift, then pull the core support and remove the LB7.
7. Stab the LBZ back where the LB7 was.
8. Swap the 03 cluster, throttle pedal and shifter with the 06 pieces.
9. Work my way through the required wiring changes.
10. Power up the system, use the V2 to reflash the ECM.
11. Prime the fuel system, fire it up and live happily ever after. :happy2: