Okay! Why couldn't I find that?
So if we believe the pics that Parts N More shows, Ken clearly has the earlier sprocket. Either (A)Parts N More is wrong (somewhat likely) or (B) the PO swapped the innards of the tranny into his block (also somewhat likely). Either way, I think a phone call to Parts N More is in order. Getting the correct counter shaft sprocket is paramount in solving this problem.
The correct gearing is going to be difficult if theory (B) is correct. It would be unlikely that the counter shaft would be the only thing swapped in. And the two transmissions in question are surely different, considering the difference in tooth # of the sprockets.
I'm sure my pontification is only raising more questions. And probably ones that can't be easily answered. My advise is to get the correct spline sprocket and ride it and see if it is what you want. But make up your mind quickly, like no more than 100 miles or so. Chain and sprockets wear at the same rate, and getting one of the three pieces out of sync will make all of them wear out prematurely.
In regards to chain size, back in the day when people made their bikes make more power, the chains of the day were not as strong as today's chains, and needed to be upgraded to larger sizes to handle the new found power. Metallurgy has improved since then, so the only consideration should be that all 3 pieces fit each other.
Fake edit; You posted while I was composing, Ken. Your figuring is a bit off. Your motor is the 794th, not the 20794th. The idea was that the very first bikes off the assembly line had matching numbers(engine and frame), but as time goes on a few engines were rejected, so by the time they got into the hundreds, they didn't match anymore.