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As long as you have the bell housing from the 86 manual it will bolt right up onto your 90. The other thing you need to look out for is that you'll need to get a clutch kit and flywheel for a 86 and put it on your 90. They will bolt right onto the block just fine. But the clutch/flywheel that fits a 1990 will be too big for the input shaft off a 1986 4-speed.
I've done the opposite of what you're doing, I put a transmission from a 1990 onto my 1986. One thing that made my life 100x easier was using the cross member that came with the transmission I was putting in, not the one that came with the truck. In your case, that would be using the crossmember from the 1986 on your 1990. Drive shaft lengths is another thing to be wary of.
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