If a bearing makes noise or binds at all...replace it now while you have it apart.
I replaced to actuator arm bearing when I did mine, it was not hard to do with the cases split. Just CAREFULLY tap it out from the underside with a punch or screw driver and press the new one in with a similar size socket. You just need to keep from scaring the machined surface with whatever you use to tap it out. You can get the bearings from any Yamaha dealer or anyone who carries OEM Yamaha parts.
#2 Gas is fine, but I'd be careful with the Acetone. Simple Green, Carb cleaner, and a Tooth brush go a long way. And don't skimp on the elbow grease. lol
#3 If you think a bearing doesn't feel smooth and quiet when you turn it...Replace it. They can be a little pricey, but not nearly as bad as what a bearing failure can cost.
#4 No need to replace the studs unless they're bad and absolutely need to be replaced. New studs are nice, but you can run into more problems if you break one off or strip some threads.
Good Luck, and take your time. There is no such thing as too clean, I treat it like heart surgery if you know what I mean.
Welcome to the BHQ!
-Ryan