As far as greasing certain parts during the rebuild process, about the only parts that need grease are the bevel and clutch gears, the clutch cam and the bucking bar and ball, you'll get all kinds of opinions on marine grade, Lucas red n tacky, moly greases, and lithium greases.... Of all the ones I've tried over the years, my preference is Kendall super blu, it's a lithium complex grease that's water proof and it's not super sticky like the red greases but it stays put just as well. This stuff works great for the gears and the clutch parts like the clutch cam, bucking bar and ball. If you prefer the red sticky grease, it does work good on the gears since it stays put and it's really thick so it helps quiet the gears a little, but the gears will usually quiet down on their own after the bike has been run for about an hour or so.
You don't need a lot of grease on the gears tho and it can't come in contact with the clutch pads, just a small dab on the gear and it'll spread over all the teeth quickly once run.
This is the stuff I use on everything from the bevel gears and clutch parts as well as the brake and clutch cables on these bikes to the bearings in high end cars or heavy duty trucks... it's just a really good all around grease, it's waterproof, it stays put, and it protects the parts very well, even after 30k miles in a bearing it still looks like it was applied yesterday... http://www.petroleumservicecompany.c...super-blu.html
the stuff can be hard to find sometimes but I get it off eBay in 1lb tubs for about $6 per tub and a 1lb tub will last about 3 to 6 months at the shop so it would last year's in one's garage...
Here's the ebay link I get it from if interested... http://www.ebay.com/itm/141658016531...%3AMEBIDX%3AIT
There's no need to grease anything inside the engine but a thin coat can be applied if an engine is to be built then stored for a really long time to prevent corrosion, it'll keep things like new until the engine is ready to use then the fuel/oil mix will wash it out as the engine runs for the first few minutes, this step isn't needed unless the engine has to sit for several months unused in a very humid environment. Otherwise just a small amount of motor oil on the bearings and rings will be ok, the motor oil will stay put and protect the bearings etc for several weeks inside a closed engine. Some people will spray a shot of wd40 into the cylinder before starting for the first time just to lube the rings until the fuel oil mix can get in there.