Hi..I see your dilemma. But, as you have kinda stated that you would like to rebuild the '86 shell, that really means that you can't use the gearbox from that to do an auto to manual conversion on the '84 car. So, it looks like you really have two project cars here! The conversion to manual is pretty straightforward but can be time consuming and expensive. You will have to change the bellhousing on the engine (or at a minimum fit the clutch release lever assembly), fit a set of clutch plates and a thrust bearing and possibly a new flywheel. Fit the clutch hydraulics and a pedal box. Fit all the gear rod linkages and I think you might have to change the drive shafts too as they might be a different length on the auto transaxle to the manual one? I am sure someone can advise here. I think that generally when someone tries this they literally tear everything out of a donor car (box, tube, engine the works) and move it all across. Alternatively, they simply sell the auto and buy a manual car...
If it were me, I would stick to keeping the cars as they are, do the welding and any other work required on the '86 to get that up-to-scratch, then find someone who is breaking an early car that has a good interior and get that for your '84.
Not sure if any of that helps you out..but good luck with your decision!