A good friend of mine is just doing the opposite, he has an '82 50hp longshaft and is using an older shortie mid-section & short-shaft L/U to make a motor for his 15" transom GW Invader.
After doing some research, we established that the powerhead base gasket from around '66-up 50hp engines was the same part number. Therefore, the powerheads will all mate up to exhaust plates of any years therein.
The thing to do on yours would be to pull the entire 50hp short shaft powerhead, including lower cowling, and slap it onto the older 50hp longshaft mid-section.
You'll definitely need a new powerhead base gasket. I would recommend replacing the tuner-plate-to-mid-section gasket as well, since it's likely to be disturbed by all the commotion. Wouldn't be a bad idea to renew the upper water tube rubber grommet (in the exhaust plate) since it's very common (especially on salty motors) for debris to build up around the grommet and squeeze the water tube shut.
We also found there were some differences in shift linkage (solved by getting the appropriate-year shift arm) between long & short engines, but eBay provided the correct part, even though it's now NLA. If both of your motors are intact, you should have all the parts you need to do the swap.
I really don't see any big issues in getting this done, besides the labor involved and a few consumables.
Hope this helps, and let us know how it goes..........ed