Re: swapping parts
you'll have to scrouge up a column and linkage, cooler lines, tranny mount and another floor cover, or just patch the one you have. If thre are no cooler connections in your radiator, you can just put an auxiliary cooler on and keep your radiator. I would recommend an extra cooler anyway. Hopefully, you are keeping the D20 transfer case or using another one with a center rear and right side front. you may have to change shift linkage since the T400 is longer than the 3-speed. the tough part will be mating your tranny to the TC. the original d20 adapters are getting scarce. The rear crossmember may have to be relocated for the longer tranny. Check the flywheels too. I think they are a little different.
the windshields should be the same. I don't know of any change over the years.
J4000- 8ft bed, 132 wheelbase, 1/2 ton
j3000- 126 in wheelbase (early models)
You mentioned a '77 wagoneer. Is this the parts donor? You may make it easy and use the QT transfer case but you'll have to get an offset rear axle. Part-time kits are available for these units. If you're doing this swap for mileage, it's probably not worth it. There won't be much difference and I've heard autos are worse because of torque converter slippage. If you want everyday drivability, then go for it. Good luck