This is where the "Spec" number on the motor ID plate comes into play. Onan, Kohler and other engine manufacturers made the same core engine type but customized it for use in different applications. As you rightly noted, the output stub of the crankshaft is one of the "customized" areas of the engine. Stubs could be splined, tapered or straight with a keyway and they could also be made in a variety of diameters and lengths. I can't tell you what Onan supplied Sears but most likely it was a straight shaft with a keyway in it and it was longer than what Case spec'd. The thing is......this is usually not a problem. Long shafts can be easily cut down and if the diameter is different, then you just use an appropriate Lovejoy coupler half to fix that problem.
The other issue will likely be a difference in the oil pans but this can be solved also by swapping the Case pan to the Sears engine. Another potential issue might be the output of the alternator but once again, the stator coils could be exchanged if the Sears unit is less than that of the Case. If you can get the Spec number of the Sears engine, I think that Boomer should be able to tell you what all the differences are. :thumbsup: