The Nutter bypass is not a CA smog legal modification on the 4.2L YJ. Even if a smog tech doesn't notice the stealth mod, chances are you wouldn't be able to tune the Carter BBD well enough to get the emissions levels low enough to pass smog. Having a functional stepper motor is key to passing smog. The whole Rube Goldberg feedback carb contraption was made like it was so that it could pass smog, while normal carbs would not.
You need to verify that that the Coolant temperature switch circuit is closing at 135*F, and that the Thermal electric switch circuit is opening at 65*F. Until both conditions are met, the computer remains in open loop and the stepper motor will not function. I recommend you either build yourself a diagnostic reader or follow the "quick and dirty" checks on the Adventures Under the Hood site to test the sensors. That will tell you if either part is faulty. The method of the quick and dirty checks will also test the wiring. Find out which part doesn't pass the test, and then replace it.