Hey Dickie and Jeep, Putting a 350 in a jeep has been done numerous times, A buddy of mine is doing a 350 into his willys jeep, THere are many conversion kits for this type of swaps.
Also Dickie if you are going to rebuild it, don't go stock. If you just want a stock 350, go with the reman 350, Most can be picked up for under 1000, I have found one at checkers auto for 695, and they have a 36/100,000 warranty with them if I remeber right. Thats a he** a lot cheaper than trying to rebuild stock.
Just don't give up on this, you will love the new power you will get from the jeep with the swap.