So far I have taken the alternator cover and one of the side covers to access the crank shaft. It turns over smoothly with a wrench. When I turn the crank, the alternator also spins. Does that tell me anything? The gear that the starter would crank on turns over easily by hand. Should that one turn with the motor?
Very good testing!
Yes, if you turn the crank over, and you see the alternator turning at the same time...then this indicates that the alternator chain/starter chain is not broken and is functioning.
The gear that the starter would turn, should spin freely one way by hand. But should not spin at all the opposite way by hand.
As for the transmission, when the motor was in the bike it would shift through the gears fine. Can you determine anything from that without having a load on the tranny?
This would tell me that the transmission is functional and that it was put together (if ever apart) correctly. It would also indicate that the shift forks are functional too.
It does not indicate how much wear is on the shift forks or on the transmission.
Also note: Not being able to run the engine makes it hard to listen for noises and/or knocks. Something that some folks use to determine if there is a worn bearing or gearing.