So I'm having a similar issue with my truck but I swapped it from a 47re to a NV4500. my truck is at a local shop here in town and they have had it for 2 weeks and still cannot figure it out. they said it is only going to be $160 to diagnosis but we all know how that bill ends. I would like to fix it myself. I'm moving from New Mexico to Pennsylvania on October 4th 2016 and maybe ill be able to call a few junk yards on the way to see if they have a PCM. But I don't know if that is my problem.

 

Having the same problem, did you ever figure out how to run voltage regulator to make alternator work , i am about to pull my hair out

 

search youtube for Cummins external voltage regulator ...I used the adjustable reg..lighting will surge..but charges well now..