If the battery is known good and jumping right to the starter doesn't help, chances are the old 2-brush starter isn't doing so well. I think they can be rebuilt, but it might be a better idea to get a more modern 4-brush style, Yamaha updated it after a couple years due to hot start problems since the 2-brush was very marginal torque wise.
I skipped a gasket on mine and used black RTV....mine spins as strong as ever afterward. The trick is to NOT tighten it right away and squeeze all the stuff out. Apply a bead to BOTH sides, then just put the cover in place...the flywheel's magnetism will just hold it in place. Wait a full 24 hours(assuming warm weather), then tighten the bolts and refill with oil. You also need to be very sure ALL the oil is cleaned off the surfaces and covers, so that no oil will drip into the silicone as it dries...the oil will prevent it from curing right IME.
I suppose if the re-used gasket isn't leaking no reason to worry, on my '97 all the side cover gaskets ripped to shreds pulling the covers off. Bitch to scrape it all off.
I'm not sure if you could just put the gears/axles in place without the side cover on and try cranking it so see if it spins better.
Welcome to the wonderful world of a Vmax electrical system....if you want to knock out all the problems off the bat, get a new HD stator from Rick's Electrics, a new style MOSFET regulator/rectifier off pretty much any Japanese sportbike(mine came off a ZX10...similar to the R1's a lot of people here use, but with much smaller fins), and eliminate all the harness connectors. Wire the stator directly to the r/r, and the r/r directly to the + and - posts of the battery. Stators are tricky to test, since sometimes they will only short under load(as mine did). It tested okay with an ohmmeter within spec and was putting out decent VAC, but my running voltage was still like 12.5 volts. New stator, now I have 14.4, so there was an issue.