Yes, they will interchange, but there can be different rear-main oil-control systems between the two - or not. Also, major differences in the rod-journal diameters - which poses some issues to consider.
The earlier 81A blocks used a 'slinger only' type of setup - and did not have a rear-main rope seal. On these, I prefer to replace the two pot-metal 'slinger majiggies' on the 81A blocks with the later ones that use a rope seal.
Your 81A may or may not have a rope seal (contained in the pot-metal pieces) - to check.
Rod Journals and Rods: Another thing to think about is that the 81A had smaller diameter rod journals (2.00" or so) versus the 2.139" of the later crankshafts. The 81A engines also used the 91A or 21A rods (for the smaller journal sizes).
The reason this is important to ponder is that you will not be able to pass the larger rods through the 3.062 bore of the 81A engine . . . which makes engine assembly a real *****. It can be done from the crankshaft side - but it is not easy to do (just think about ring compression!).
An option would be to have the later 59A crankshaft rod journals reground to the earlier size (something we've done with stroker setups for years) - though that can get a bit expensive.
Valve Angles and Cams: The valve angles of the 3.062 bore engines is different than the 3.187 bore engines - due to the valve locations being moved when Ford started making the bigger bore engines for the Mercury models in 39. There is a slight difference in the final cam grinds between the earlier engines and the 46 - 53 engines. While the later camshafts will work just fine, there is a very slight difference in cam timing due to the above. Most cam grinders today, don't even consider this . . . they just supply one grind for all the various years.