It sounds like you need a good electrical tech. If its not as simple as a fuse or relay. There is a tranny relay in power distribution center(PDC). If that was bad it should throw more tranny codes it would seem. I would bet it related to the charging problem. Maybe the alternator output is not reaching the PDC. It don't take much power to mess this system up. Why all you have to do is go to the parts store and say gimmi a 100 amp alterantor instead of the 65 amp stock because I'm putting a camper on it, and then the tranny don't know what to do.
TSS on a 46RE?
good luck