I would get 45 and 47.5 pilots. If you look at the chart above, you'll see that Yamaha reduced the pilot jet size to 42.5 after a couple years. There were no other jetting changes made. That would seem to indicate that Yamaha found the 45 pilots to be a bit too rich for the bike. That means they might be just right for your bike with minor mods. Pilots are usually increased one or two sizes on these bikes with minor mods, mains about the same. Remember though, yours is an early non-E.P.A. mandated set so will be richer to begin with. You shouldn't need jet size increases as much as some of the later carb sets would.
As far as straight pipes go, they're not the best choice for any engine. You lose low end and midrange power with them. They can also be hard to tune for. A muffler of some sort is best, both for performance and ease of tuning. Your early type mufflers were supposed to be the best sounding and performing stock mufflers ever put on the 650.
As far as straight pipes go, they're not the best choice for any engine. You lose low end and midrange power with them. They can also be hard to tune for. A muffler of some sort is best, both for performance and ease of tuning. Your early type mufflers were supposed to be the best sounding and performing stock mufflers ever put on the 650.