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1. The transmission clunking is very common. New oil usually eases this a bit. Changing to synthetic oil almost eliminates it, except for first gear. There is really just now way around that one. The clunking isn't something to be concerned with. Grinding, however, is something to worry about.
2. I doubt that you bent the actual swingarm. That's the thick black metal framing that supports the rear wheel. When you say the rear brake swing arm, I'm not sure that I know what you're talking about. There is a long/skinny connecting rod, a little spring, a brake light sensor and then you start getting back up towards the front of the bike. A better description would help.
In regards to setting preload on your rear shocks, there are numbers on the slots. 1 being the softest and 5 being the stiffest. Once you get to five, you can drop it down into 1 and start all over, essentially trying them all until you find one that you like.
I prefer 4
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