I need some help here guys....

I recently changed over my 06 cummins to a ford style manual fan clutch. I did quite a bit of reading on it and found that the electronic fan clutches are prone to problems (are very expensive) and that the only real downside to the manual clutch is that the ac might not be as good at an idle. Great. Did the swap fired it up and all of a sudden the check engine light is on and the truck is stuck in third gear. Called the guy who built the transmission and he said that the governor solenoid uses the fan clutch as its 5v reference. How is it that I seem to be the only person on the internet that is having this problem, and what can i do to fix it, hopefully without having to revert back to the electronic clutch ?!! The only issues ive read about, is that doing this creates a soft code that shouldnt even trigger the check engine light and has nothing to do with the transmission.....

I appreciate any help you guys can give me, cause im at a loss here.