For some reason, I have a hard time tightening the bolt that holds the Exhaust up. It's like the clamp that goes around the exhaust is not long enough, so when I tighten the bolt, it squeezes on the muffler. Now that clamp is already pretty tight, and there is still alot to go on the bolt.
Right now, in order from outboard to inboard it goes; Bolt, clamp, clamp, exhaust holder bracket, stock washer, nut.

Also, is there a trick to getting that rubber piece aligned, that goes between the muffler and the clamp? I have a really hard time getting it straight while trying to align the clamp.
thanks

My bike is too far away right now I can't look and tell you exactly how I set mine up but I definitely remember that I didn't have any issues with clamping the muffler down.

Check out this thread maybe it'll help
http://www.ninjette.org/forums/showthread.php?t=10272

By looking at your last picture I can tell that you don't have the rubber liner properly installed to the clamp. It wasn't too big of a pain when I did mine but I remember that all of the edges of the metal clamp should be covered. Try lining up the ovals on the liner with the clamp then make sure you press them in firmly. The outside edges of the clamp should be covered by the liner, also my liner was a little long so I had to cut off maybe 1/4 of an inch or so. When it came time to actually putting the clamp on the muffler I just slid mine on instead of pulling it apart. Then I brought it down so that it would lay flat on the muffler and pinched it with my hands, it held the muffler snugly and the clamp ends came together without any need for brute force.

Your other pictures don't show much except that the bolt sticks out. Do you have the muffler aligned properly? Maybe the bolt is going through the bracket at an odd angle. Is the clamp positioned properly on the muffler? From the last picture it looks a little close to the label. Also are you putting on the clamp correctly, it's shape makes it fairly easy to put it on backwards.

Hopefully that helps. If you're still having issues snap a few more pictures of the muffler that show how it lines up with the bike and how the clamp lines up on the muffler.

Sorry this is long.

You def need to get the rubber piece lined up. On mine there was a way to do it backwards and then none of the holes lined up. Try flipping the piece around.