Yes there is, the auto trans controller will speed up the idle slightly when you put the car into gear. The manual trans controller may let your engine stall when coming to a stop or putting the car into gear. Also, if you are using a late ('94 ) 999/32RH automatic with a lock-up converter, the manual trans upshift indicator light circuit and the auto trans lock-up circuit are on the same pin of the controller, which will cause weird shifting if you use the manual type controller. If you use the Auto trans controller, you may have a poor idle or incorrect fuel mixtures/stumbles with a manual trans. If you can't find a proper controller used, there are rebuilt ones available at the dealer, roughly $250. As far as the wiring goes, Mopar Performance has made the wiring from the MPI kit available for sale separately from the kit. It's in the 2000 catalog. Hope this helps, good luck!