You're probably running the air pressure in the shocks a bit low and the shocks are bottoming out. For just you on the bike with no load, I'd try 20 psi...with a passenger and loaded, you'll probably need to go up to 40 psi or a bit more. I had an '06 SEUC, just a different color, that I put 25K on in two years. For me, the stock seat sucked, so I changed it to a Corbin Dual Tour (heated). The foam collapses on the stock seat, IMO, and you're sitting on the pan (driver)...the passenger portion is OK. Others never had a problem with the stock seat, but it would KILL my tailbone after about 100 miles or less. There is nothing special about the '06 brakes, other than the stainless lines...they do make a difference. You've also got "floating" rotors in the front, so that makes some difference as well. The newer model bikes have ABS and Brembo calipers...they are 100% better than what was on the '06. It all depends on what you have to compare to. I ended up with Rinehart True Duals, Doherty PP air cleaner, and a Powercommander, with a GOOD tune. If I was cruising on the back roads, two up and loaded, at about 60-65mph, I could get as much as 44 mpg. By myself, taking it easy, I got as much as 48-50 mpg. If I was riding hard, it would drop to 35 or less. Mileage suffered at anything over 3K RPM when cruising, which if memory serves me, was about 75mph. My bike never pinged, and I live in Alabama, where summer temps get above 95 degrees regularly.
The '06 103 is a different motor than the '07-'11 96" motor with the 103 "kit"...two different animals entirely. The old 103 was a rock solid engine with the exception of the Cam Chain Tensioner shoes, which need to be checked at about 25K for excessive wear...if they go out, the whole motor can be taken out. You can either replace with new shoes, or replace with the newer style chain tensioners (better alternative). Here's the short list of things I changed on mine: Seat, handlebars, brake calipers (PM calipers), Legend Air rear shocks, Traxxion Dynamics front fork cartridges/springs, windshield (Clearview with recurve), heated grips (Heat Demons), wheels (PM wheels...for looks...18" front/16" rear), exhaust, air cleaner, Custom Dynamics LED strip on the back of the leather Tour Pak (run and stop), CD LED tailight, added Garmin GPS with Techmount handlebar mount, modified radio to have another AUX port in the rear of radio so GPS could "talk" through the stereo/headsets, J&M shorty antennae. LOVED the bike, but financial issues forced me to sell, and I took a beating. I'd still have it otherwise. You've got a great bike...enjoy it and make changes you feel are needed to make it fit you, if any. The stock heated grips are a crap shoot...some last, some don't. If they go out, just put Heat Demons in and be done with it. There are a lot of threads on here about the '06 SEUC...it's a great bike that you can go as far as you want with modifications. Enjoy!