From what I have read all the controllers are about the same (there are differences for throttle versions). A couple members have successfully removed the voltage cutoffs. I too would like to use different batteries. I would like to go a little bigger if possible (15s battery) though. To alter the firmware you need to make a custom cable and use a computer program. It does not have an interface that shows settings that you can change, you have to actually edit the firmware file / code. The code is not clear and it has values that mean something that you must investigate to figure out what it is, it was not made to make it easy to hack it.
A couple people have stated 500w and 750w units are the same too, just different amp settings. The 36v unit has a different motor that operates at 36v. If you were to run your 48v unit at 36v it would (I believe) have a lower engine max cadence rpm (maybe 70 - 60 depnding on battery charge remaining), but a 36v unit with 36v motor will have 90 cadence rpm with a 36v battery.
The motor amp settings on the vlcd5 do not work either. Firmware is stored in the controller not in the lcd.