Timing gear chunks. Original timing gears were nylon coated. When you buy your cam buy a new timing set.

Typical for man bearings to have those grooves. If you're just doing a hone'n're-ring, I would replace main and rod bearings. If you desire, you can bring the crank to have a machine shop to have the journals inspected/polished. Add a high-volume oil pump too.

Yes, sounds like you have a ridge. I wouldn't worry about it. I would hone the cylinders with a ball hone then I'd give it a set of new cast rings, I prefer Hastings for this job. Cast rings are more forgiving to hone grit and bore taper than moly rings.