With what you've just added to the "equation",I don't think you realize just how involved this might be. There's the ignition assemblies, alternator assemblies, crankshaft assemblies, piston compression heights (that depend upon connecting rod length), piston domes (that depend upon combustion chamber type), to consider.
For example, if you try installing a 12v era top end on an untouched 6v lower end, the 12v piston will sit far below deck height at TDC. And, you don't know the condition of the used 6v crank assembly. If you attempt to install a 12v crank, to mate with the 12v top end, compression height will be correct, as will piston type...but what will you use for ignition & an alternator? Can't use a 12v alternator with a 6v crank, nor a 6v alternator with a 12v crank. And the CDI pickup won't fit a 6v case half, without mods.
Going with a used, "sealed", lower end without opening it up for cleaning & inspection is huge leap of faith. How do you know the condition of the gears, shift forks & crank assembly...or how clean/dirty it is internally? If there's any sand inside, the engine will shred itself almost instantly.