If you're doing 5500 rpm in 5th, you're moving down the road at a not so legal clip. Yes, there are some sweet spots and buzzy spots over the full range of rpms on our bikes. One thing you might try is a 17 or 18 tooth sprocket to move the sweet spots towards the range of your riding style. You can also look into handlebar vibration dampening fixes.
When you ask whether Thunderbike pipes will "do a better job", just what are you looking for? Is it better performance, better sound, or something else? Regardless, there are a ton of threads on the topic, and you can find them by using the search engine.
Overall, it sounds like you've been changing out some mods on your bike that you aren't happy with. Do some reading on these forums through the archives using the search engine to find possible ones that you might like. It can save you some money. I've found dealers to be sorely lacking for any knowledge about fixing minor comfort issues using aftermarket parts. Around here though there's a wealth of information from actual riders who've tried numerous methods to make the bike more comfortable for them. It's one of the best things about ba.com.
Let me know how that gel seat works out for you. I've heard their high heat retention make them a poor seat for us desert dwellers.
