I work with a structural engineer that owns an either 88 or 89 wrangler. His son (Yoshifab) put in a 3.9 cummins 4BT. He's had it now for several years and loves it. He has told me that a hot ticket now is a used Jetta diesel engine (don't remember the size or years). However, from what I understand it is a lot of work.
on extreme 4x4 they put a 1.6l jetta diesel and put a greese engine kit on it which let it run on diesel and vegetable oil. very very good on gas mileage and plenty of power if you put a little research into the engine and what to put in.
I would definitely look into the 4BT. I love mine! I worked for Novak for a summer and drove every V8 powered Jeep there is, and there is just nothing like the 4BT, you get tons of torque and power, and you can get great fuel mileage!
PM me if you are interested in some motor mounts for the swap or check ebay.
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