Since I've never done this I don't know for sure, but I expect that the flywheel and trans will bolt up okay. I do wonder, however, if the crankshaft end is different on a manual in order to take a pilot bushing. I know that the diesels are.

If it is not leaking you don't need to worry about seals. Since there is no slip yoke on these units that is not typically a problem.

I have no idea about throws. I've never driven an 86, only my 88 and the shifter is just fine. I've driven stick shift cars for well over 40 years now, so whatever shifter characteristics are present I just drive it and enjoy it.

Have a great day,