My 09 has the Rush slipon mufflers with the 2" baffles. First the top end noise. It is there but I believe this is just the way it is although I to worried about it. After 1700 reliable miles I have stopped worrying about it and started enjoying the bike. Admittedly my 08 SG is very quiet mechanically but I have had several HD guru's listen to the 09 bike and say "all is well". As to the heat management system. It is there and when I first got my bike it would kick in at almost every traffic light. Don't believe anything is being hurt by it shutting down the rear cylinder. That's what it was designed to do. As for tuning. I have the PCV from FuelMoto and couldn't be happier. The rear cylinder still shuts down but NO WHERE NEAR what it did before. It takes a hot day in a lot of traffic to activate. My mileage increased with the PCV, though I was told it would drop just a little. If you like the looks and handling of this bike and are just worrying yourself about that top end noise then I would go to several dealers (HD or Independent shops) and have them take a listen. I'm thinking they will calm your fears. If they don't, then get rid of the bike. Peace of mind is more important than any motorcycle. Lastly, while I had some doubts about this bike initially (It just didn't fit me. Now I've grown in to it) I enjoy it more and more every time I get on it. Hope it all works out for you.
Gary
P.S. I talked to my local tuner who installed a SERT tuner on my 08 SG, about the PCV. Just talk as I am very happy with the PCV as is. He did mention he could do a lot with the bike if it had the SERT tuner. $359 for the tuner and $295 dyno time. This might be an option for you if you keep the bike. Also try this trick though it may become tiring. Hold you legs against the fuel tank. It eliminates a lot of noise.