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from the UK Nathan.
Apologies if you've addressed some or all of these already, but less chance of missing anything out if I assume that you haven't.
1) Note down the frame and engine numbers and then go to the VIN tables in the Tech Library (see toolbar above) to determine which model you have. Theses two numbers would have been the same originally, but engines do get swapped, so look up both if they are different.
2) Once you know what you have, you can download parts and service manuals from the Tech Library.
3) For engine parts, I would start off looking for genuine Yamaha on Partzilla, CMSNL and fleabay, using the part numbers from the manual. If you need a re-bore, get your engineer to tell you which oversize he's going to have to go to before ordering piston & rings.
4) If the carb is a Mikuni, don't use the brassware out of a carb repair kit - most original parts are still available new from Mikuni and Yamaha. If the carb is a Teikei (TK) your options are more limited.
5) Switches and indicators were shared between many models - maybe post photos of your bike, to show what you have, and we can take it from there.