1: Normal. The bike is jetted exceedingly lean from the factory. Drill out the A/F mixture screw and then do the white spacer mod. All very well documented in the Tech/Reference section.
2. Normal. The stock brakes squeal like a stuck pig. Either learn to live with it or put on a set of aftermarket. The EBC reds are very quiet and stop quite well.
3. Normal. The belt drifts from side to side on the pulley (depending on the lean angle on the rear wheel) It is normal for an otherwise properly adjusted belt to make some noise after a long ride. Push it around tomorrow after things cool off and you won't hear a thing.
General maintenance tip, the belt tension should be checked every 2000 miles. Again, all the info you need is in the Tech/Reference section.
4. Seat comfort. Good luck. Even with a $400.00 custom fit gel seat, my butt would still smart after an hour or so. You will have to do some fabrication to get an aftermarket one to fit.
5. Pillion seat comfort. I told you so. You can try this
http://www.seatsaddle.com . It helps, but not alot. The pillion is too small, too narrow and the back rest is too short for long distance rider comfort.
There's no cheap answer for your complaints. The spacer mod and the A/F mixture you can do. Everything else is going to need alot of coin.
You should have gotten the other bike. The Savage is the wrong bike for 2 up long distance riding....