Yep- typical gear condition, but serviceable. Years ago someone told me the pits carry extra grease improving lubrication. Sounds good to me. I believe the driveshaft assembly changed from 26 to 27 as it connects to the crankshaft. I’m not familiar with any other changes. I suspect your correct on your assumption of the fibrous goober. I don’t believe its factory.
Restoring the surface. A polish is the least aggressive. Keep reapplying and rubbing till it doesn’t get any better and you have removed the surface corrosion, reviling the original finish. I’m always trying different stuff. The Zephyr is different than all others I’ve tried as it drys to a haze that is easily removed. I find 0000 steel wool useful. A little more aggressive. I often use it on carburetors. The staining, where moisture has etched the aluminum, requires a much more aggressive approach. I get this 3M paper from Home Depot. Its the best I’ve found for wet or dry sanding. It’s available from 120 to 400. I wish it was available in finer grit’s but I can’t find it. You’ll want to use sanding blocks on parts like your gear case. After the 400 I go to the buffer. Ive been polishing since I got my first motorcycle in 1965. Every hobby I’ve been in has had aluminum to polish. If you want to try to learn how to remove that deep staining and restore the surface, start with something that is no longer usable or easily replaced. Its dirty nasty work and its no fun (for me anyway). Often the contamination in this early aluminum leaves you with disappointing results. Except for the flywheel I believe the rest of this motor has just received a hand polishing. Been a while.
A "Boathouse Repair" is one thats done without having tools or the skills to do it properly.