The whining will have come from the gears not running parallel to each other, which is usually form worn bearings, or with the drop gears, from misalignment. They will usually only do it when loaded up, so if it was only doing it in say 2nd gear, I'd be looking closer at this gear and how it's mounted. If it does it in all gears, then it's either the Drop Gears and / or the Final Drive.
As Alex mentioned, there's no balls missing from the Mainshaft Bearing, it's only that the cage has gone that makes it look this way. This would almost be certainly the issue with it dropping out of gear.
None the less, all checks should be made while it's in bits, replacing all bearings, Layshaft and what ever else is worn or damaged. The maximum allowable clearance in the Shift Forks is 0.015", however, when buying a new one (if it's needed) take your hubs with you and check them on the counter. Many I find are out of spec, right out of the bag.
What I can see of the Dog Teeth on 3rd Gear still look OK. These heed to be 'sharp' in shape, and not rounded off on the lead in side. Same goes for the Outer Track of the Hub. I have had the best look I can at your photos, sorry I find them not quite clear enough, they appear to have a good shape, but I think they are chipped ??
This is about the best photo (as in clearest) I have;-
While these are not chipped, they are well worn and right on about the limit of what will still - just - work, though, personally, I wouldn't refit it