You can't really rely on the manual entirely today as the lubricants they had then were much different from what we have available today. Originally they called for straight 40 in average conditions, 50 in temps above 90F and 30 in cold weather.
IMO, these like a thicker oil, such as 20w-50 (straight 50 can be difficult to find). Equally important is to find oil with a higher zinc content. "Racing" oil usually does (I run Valvoline in mine) or diesel oil. Note that these bikes have a dipstick with a wide range of capacity between 'full' and 'add'. Keep the level in the middle, not filled to the top line. Too much oil and it will start forcing it out wherever it can.
Primary side, most feel that Type F automatic transmission fluid works the best. What is nice about using ATF is it is red, so if you have a leak there it is easy to determine what part of the bike is pissing on your floor!
Gearbox is same as engine, 40w preferred. There is some belief that the gearbox just takes grease, because that's how they do it in India, but that is incorrect. A combination of grease and oil that makes a 'slurry' also seems to be acceptable.