There have been a few threads with people asking about the evo 5 speed gearbox bolting up to the VR4 block. I have got a 5 speed evo 8 gearbox in my garage and a block/box gasket from an auto VR4. So I figured I would take a photo so people can see exactly what the bolt on issues are.
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Basically all the upper bolts are in a different position. That's four bolts at the top of the bell housing that do not line up. There is one starter motor bolt that doesn't line up, but I am confident that is due to the difference between auto and manual starter ring sizes.
I hope this helps explain in the future - this subject seems to come up a lot.