Will a 1978 2E Top End mate to a 1981 Bottom?

I would say yes. The only difference between the top end of the 2e and the 81 is the head and cylinder fins are square and has 9.4:1 compression ratio where the 81 has a rounded finned head and cylinder and 9.3:1 ratio as long as you use all of the top end of the 78 and they are match from the same engine should not be an issue. Btw you would also have to swap your 81's electronic ignition over to the 78 :)
 
Allow me to amplify..

What I am considering is starting with a stock 1981 motor and replacing the entire top end (head, jugs, pistons, a new set of rings, new cam chain) from a donor 1978 '2E' onto the bottom end of the 1981 motor.

From what I've seen looking at the fiche, most of the mounting brackets and bolts are the same. Of course this would mean that the CDI would be replaced with a breaker-points setup.
 
You can put the pickup coil from the 81 to the 78 where the points go. You will just
have to make sure it is timed right.
 
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