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Only thing I can help you with is your first question. Yes, 1 ton F350 axles will fit. I know very little about diesel engines, or the Allison transmission, so I can't help you there.
Leafs are not part of the axle. I am sure you would have to fabricate mount points if you wanted to use leaf springs. My Bronco came with coil springs in the front. I have not done a 1 ton axle swap, but I know it is the same width as the Bronco front axle, and the brakes will fit. Just don't know where you would connect leaf springs without drilling your own holes for the shackles.
The most used diesel engines in Bronco projects are (in no particular order): Cummins 4BT and 6BT, Powerstroke 7.3, IDI 6.9 and 7.3. There is no need for any other trans than a ZF5, pretty much bulletproof.
Tips? research A LOT, there is a ton of custom work involved in any of these swaps. If you wish to keep the project light (weight-wise) go with the 4BT.
The axles can be MADE to fit; It helps to know what year vehicle youre pulling from and ploping them in to help you out, though. There are entire forums devoted to this type of swap.
There are LOTS of diesel engines that dont REQUIRE an electrical fuel pump; Ford, Chevy, Dodge and Mercedes all have them, as well as some equipment. I put a 12 valve Cummins in mine and the electric fuel pump is just for priming the injectors. It hasnt run in months.
Dont know about the transmissions. I have plans for a ZF5 for mine, but the stock C-6 is working well for now and has been for months.
"Best," engine swap is subjective and you wont find a logical answer. I vote for the 12V Cummins.
Tips:
(1) Read EVERYTHING you can all the engines so you can figure out what you want, what's available in your area, what you feel comfortable with, what parts need to be bought for the swap and what you may need to cut to get it to fit in there.
(2) Unless you move the drive train back, a 12 valve C-6 combo will give you 2.15" of room between the crank pulley and the radiator. Plan your fan accordingly.
(3) Stick with the coil sprung suspension.
(4) Plan on adding hydroboost while you have all that garbage out of the engine bay; Hands down the best change I've ever made on my Bronco.