Yamahas seem to have a lot of reasonably-priced NOS parts available, both from eBay as well as Speed & Sport (the Yamaha dealer on the USA east coast, not Matt Hilgenberg's S&S in California). Some of the Japanese manufacturers seemed keen on clearing out their inventories as soon as they could.
I think the best bet is to budget more money and then go looking for a bike where someone else has already done all the hard work restoring it and now wants to move on to another time/money pit.
Let them spend the time chasing parts, repainting, etc.
If I'd bought more nice ready to ride bikes over the decades I would have gotten orders of magnitude more riding done.
Of course, you may still want to strip even a nice bike to check for DPO (dreaded prior owner) issues that weren't dealt with, but a quick dis/re-assemble is a lot different deal compared to a ground-up restoration.
There are also times when you'll be time and money ahead if you just pay a marque expert to do their marque expert's magic instead of screwing things up on your own.
If you can get access to parts books be sure to get them along with a good (preferably factory) service manual. There are often parts shared across a wide number of models, and you may find that you'll spend a lot less on Part #333 from the plebeian trail bike than you will on the same part advertised for the MX model. You might go weeks not seeing the part listed as for the MXer on eBay while in that same time there have been 5 of them listed for the more common bike.
cheers,
Michael