Well, I dunno what part number ARB or Detroit you have, but most of the time 4.56 and 5.13 or 5.38 will run the same carrier.
What Dana 44 front do you have?
I can change out a trans, I understand the basics of gears but haven't done them. But the 4500 is going to be more than just changing out a trans. As it was pointed out earlier, there is no room for a 4500, the clutch fork and slave cylinder will have to be completely reworked, it will want to protrude into the tub, etc. If the setup came from the friend with the clutch and stuff figured out, then maybe it can work more easily, but there is still the clearance issue. Not sure how your friend made room for it in his Jeep.
Not sure how you're breaking gears but that isn't typical, even on 5.38s. If they're set up properly and the axle is sized appropriately, shouldn't ever be a problem. I don't think a Whipple will fix whatever you are looking to fix....what was the actual goal with all of this?
Not saying you have a barbie jeep. I will say, the Atlas II is actually helping your AX15 and clutch also. The lower the gearing in the transfer case, the less stress the engine and trans see.