One thing I have not been able to determine is whether or not I need to return the truck to stock, then update the controller, then reinstall the programming.

I have the SmartyJR currently installed, and see there are at least one, if not two, updates. I saw mention a while back that the updates help with smoke, so figured I'd give them a shot.

Do you need to unload the software from the ECM before you update the handheld unit? Or will it figure it out?

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I figured it out on my own...