Adding racks won't hurt anything if it's done well. You'll have to drill a couple small holes in the rear fenders if you're using a 200ES rack. You need, or need to fab the support brackets for the rack, that go under the fenders. You'll have to do fabrication to the frame too to make it all bolt up.
The front isn't too difficult to do. Several people have posted pictures of their 200ES front rack and headlight on 200M forks. Those should give you some ideas. You'll need a large drill bit to drill holes for the rubber mounts in your brackets, approx. 5/8".
How much crud was in the oil cleaner when you pulled the centrifugal clutch off? That stuff is usually packed in there hard, they typically don't ever get cleaned out like they need.
The stem bearings are actually available at local bicycle shops. I don't remember the size off hand, but they're just a loose ball bearings and bicycle shops keep those in stock, for multiple sizes. If you don't want to spend for tapered bearings, and have a bike shop nearby, it'll be all of a few bucks to replace the bearings. They used to be 5 cents each at places around here.
That's great about the seat pan. That's a big money item if it's roached.
The decompression cable is suposed to go from the recoil starter, held to the center of the engine case with a little clip bolted on next to the vent tube, to a clamp on side of the cylinder head, and attached to the decomp lever.
The hand lever is really just a parking brake. Should be a little clip, on the perch, that holds the lever in. It doesn't have near the leverage of the foot pedal. I guess if you ride wheelies a lot, it'd come in handy.
The story of three wheels and a man...