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if your going to keep the same trans then you need to stick with the 351/400m or a 460. otherwise you need to change the bellhousing/trans for something else.
What are your plans for the truck? The stock engine thats in it will likely give you less headache down the road. I have a heavily modified CJ with parts/components from a Ford truck trans behind an AMC engine, Chrysler fuel injection, GM alt, Nissan fuel system parts...... While I wouldnt change anything I've done to it, it can be a pain trying to remember/keep track of what's what when I have to wrench on it. For this reason, I'm leaving my Bronco as stock as possible
It's best IMO, to keep the Bronco as stock as possible. even with the age of your Bronco it might be harder and harder, but it's going to be easier to sell knowing it's all stock.
I have thought of that question also, I love my 88 XLT, 351 EFI but I thought this would be a great upgrade, 3/4 or 1 ton 2005 or newer 4X4 super duty. Basically the whole drive train, master cylinder, brake booster, steering column, steering box, torque converter, trans, motor, radiator, wiring harness, computer, and both axles. I would also be able to upgrade the drive shafts and u joints. I am not sure but I think the rear axle is already disc brakes, if not already make it disc and upgrade them to better aftermarket discs and calipers for better stopping with bigger tires. I know this would be a very long, and expensive project but it would be easier to find parts for, and it should still be in great shape to give to my grandson when he graduates high school.