V6 and 4-cyl trans and t-case are different. You should be able to swap the engines around, being aware of the different plates that mount the bellhousing to the block. I'd leave the automatic in and work with it, but if you want to convert, you'll just have to move all the pieces from one truck to the other...wire looms, trans cross member, etc.

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1987 Raider - Roxy
1988 Mighty Max 2.6L Turbo - Pearl
1997 Mountaineer V8 - Freddy
2000 Excursion V10 - Freya