Ok; thanks to you guys' input, and because I have a short break in the other fun stuff I've been doing lately, I bought some stuff today.
Yesterday, I asked an "engineer" type friend from work to please come put his eyes and his brain on left case, the bearing, and the output shaft...I just needed confirmation of what I should do next. He agreed, and we spent a good hour really inspecting everything, concluding that I should definitely use the new (used) left side case. It really wasn't a "no-brainer" until we took a close look at the output shaft. He confirmed my findings that it is, indeed, bent (and that it wasn't going up and down because the bearing had been smacked cockeyed). But more than that...check out the splines where the front sprocket rides!!
For comparison, here's what the new (used) shaft looks like:
We just couldn't in good consience use the case that took a hit big enough to do
that to the shaft, so I'll be using the new (used) left case. We also concluded that I will use the original right side case; it couldn't have taken that big a hit, and also it has the motor number on it, and if I change that, then I have to do the whole CHP / DMV thing.
The only problem with the new (used) left case is that all the bearings were "grindy". But tonight I sat down and cleaned, lubed, cleaned, lubed, cleaned, and lubed all the bearings. They are no longer grindy; I got all the dirt out of them, and they're smooooth now. I also got all the crud out of the inside of the case, and cleaned up the mating surfaces as best as I could. Then I filled each bearing (and smeared the crankshaft bushing) with assembly lube.
So I'm on my way...again.

This week I hope to get pages 3-78 to 3-86 in the service manual complete...crank, tranny and tranny forks installed; cases mated and bolts tightened, gearshift shaft/arm installed, rotor installed (before I install it I'm going to clean it up real good and add some more jbweld between the magnets if it looks like i didn't do a decent job the 2nd time I tried), cam drive idle gear/sprocket, gear position switch, and oil pump driven gear.
That's where I'll probably stop for a while, because the next part is to install the clutch. But I have a broken basket, so I guess there's no point putting it all together broken, just to take it back apart when I have the money to replace it.
Anyway, it feels good to be on the move again! It seems that I'm truly about to turn the wrenches the other way finally!