I'd suggest buying a used setup off of ebay (power brake booster and master cylinder), then swapping in a new rebuild master cylinder from advanced / pep boys.
I believe all you'll need is a brake booster and master cylinder from the same year Jeep. For a stock setup you'd need a new air cleaner (the stock non PB air cleaner would hit the brake booster), but since you have a replacement engine, you might not have this problem. I'm not sure if you'll need a proportioning valve or not.