I have the answers. The 06- trucks have a new operating system, new language, in fact, all new PCM and TCM modules from new manufacturers. Electronically, nothing is similar, right down to the harness and connector types.
That said, the 6 speed is a bolt up, along with the new NSBU. I think it will bolt up and behave as a 5 speed, as long as the connector is changed, a little pinout research I think is all. I will check with the South Pacific boys to see if they can crack 6 speed code.
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