Hi, Spooner: your bike sounds pretty normal to me. The top end of these triples sounds like someone shaking a coffee can full of marbles, normal, and the clunking gearbox, while normal, does get better with time. Mine has quieted down now, at 15K miles, where I can snick the bike through the gears very smoothly. However, when sitting at idle with the bike out of gear, dropping it into low will often still produce that distinct "clonk." Again, normal. There is a distinct vibration, or hum, in the bike somewhere between 2900 and 3200 rpm, which I suspect is due to the engine being a stressed member of the frame support system. You should notice this especially when the bike is under load in a gear that is too high for the situation. The solution is to shift down and get the bike into rpm range above 3300. As to brakes, I have never had any problem with them being soft or feeling mushy. "Bleeding" simply means to let out brake fluid until it runs clear without any air bubbles coming out with the stream of fluid. If you aren't having any problems with your brakes, I wouldn't "fix" it.
Take care,
Monte