Heres how it goes.
before you go this deal, complete the swap in the truck to a LS based motor. you will have quite a lot of wiring to do. once you tackle that and have it completed, then do the trans swap as that isnt a common thing either. Most people put the 4l80E on as it will bolt right up to the block and can handle a lot of power. you will just need to change a little wiring, a trans cross member shorter drive shaft and a few other small things, a lot easier than a alison swap.
once thats complete, you can worry about the rear, or i would supercharge it as it is a much easier thing,
but i would worry about swaping the motor and the trans in first.