I have a 3" body lift on my 48, made spacers for radiator, and 3 cab mounts, and also move the running board brackets up 2" and a 1" spacer.
And the pedal assembly I was able to make a bracket to lift it up 3" as well, so pedal geometry stays the same.
If you lift the cab, and not the pedals, then you either put new holes in the floor for them. Or lengthen the arms so they fit the original holes, and also re curve the part that does come through the floor so it is the radius of the new arm length (so it stays centered in the hole through the entire travel).
Does a 15" front driveshaft give you satisfactory angles within the range of suspension travel? Would be a real bummer to find out that at full droop or stuff that you exceed the max driveshaft operating angle and it tears itself apart.
I can't think of an overdrive like you want, closest would be a US Gear or Gear Vendors unit, but they are not ideal for a big truck, even though they say it will work...
Now, the real answer is an OD transmission, which for an Allison you have to step up to a modern computer controlled one, probably a 3000 would be good and they can be had to work with a non computerized engine. Price would be a big factor though.
Awaiting pictures,
Grigg