I haven't used an independent bed level setup on my printer but I would keep the U axis the same for your IDEX configuration and just use V and W for the other extra Z drives. I don't think you have to shift driver numbers around to keep them in order with the later firmware versions. Just pick open drivers on the Duex5 and assign each axis to them.
But again, I do run an IDEX printer but I don't use bed leveling. Bed leveling won't work to well if you do any "ditto" printing with both heads at the same time.
I could be completely wrong on all of this, Hopefully someone will chime in that uses multiple z motors for leveling.