First, throw the Haynes manual as far as you can. Then, seek and download a Yamaha repair manual and a parts manual for your year (graphics seem to be for a '77). Then, purchase a good JIS (Vessell) screwdriver before doing any more disassembly. Many of the parts mentioned are readily available (dowels, etc.) There are vendors online for many parts (Economy Cycle, Yambits, many others). You just need to do the "leg work" to find them. More major parts like the cases/covers will need ebay searching, forums searches, or finding a good welder to repair.
By the amount of rust in the oil pump cavity, I would guess that the bike has been in a flood and never drained after (in that case, the crankcase is probably full of rust, too) or left outdoors for rain water to fill the cavity - for quite some time. Remove the pump and closely inspect it. If no pitting, I would clean the outside and send it to Arrow for a rebuild. If any water made it to the crank area, it will probably need rebuilt.