I did the 44a swap, and then had to go back to the JY to get the donor jeeps front axle so I could get my 4wd back. Its probably cheaper to get both axles at once, that way you dont have to pay as much, they might give you a discount.
As for the driveshaft issue, my back had to go in with me standing on the back tow hitch ball so that it will wiggle into place. Im sitting a 3" so you will definitely want to pick up the driveshafts if possible.
"Water covers 3/4 of the earth, Jeep covers the rest"