I'm not sure what the first question is asking possibly changing the gearing will help in acceleration .
the second question about the exup , it has a warning light if not functioning properly. yes it is probably normal for the valve to be open when the bike is at idle.
the exup changes or regulates the volume or diameter or the exhaust while the bike is climbing through the rpms or accelerating . no reason for it to be full closed during idle.
the third question
try switching to the other optional viscosity of motor oil listed in the owners manual.
try 20-40 at the next oil change and see if it helps.
most yamaha's I've owned are very picky and seem to run better with certain weights and brands of motor oil.
obviously other problems are possible with your clutch or transmission, but changing to yamahlube20-40 at the next oil change is a cheap way to try to rectify the situation.