MegaSquirt (MS3) or Holley HP EFI

I have the 5.9 Magnum and Dana 60. I do have the 47RE out of the donor truck but it was a 4x4 truck and transfer case is in place of tail shaft and housing so was going to go another route. Just unsure of which transmission. There is a 904 in the car now, so to at least get it up and running will use that, but ultimately want to end up with overdrive automatic.

8HP70 out of a charger! Built in transbrake and manual valve body.