My turn signal does the same thing--I believe that there is a plastic piece behind the steering wheel that broke or wore out. I have not been motivated to check it out since I am now used to it.
The shifting in 3rd (called by many "snicking") is pretty damn common with the R380--the LT77 does it from 3rd to 4th. Get used to it--it is a bonding experience that we all must go through, like a new girlfriend.
I don't worry about the mud on the pipes, but if you want it cleaned off, then I would suggest wire brushing it off. What a pain that would be, though. When you go through mud, it will stick and then dry pretty rapidly.
Remember, when you find little things (and there will be many), just keep telling yourself it is a bonding experience. Between you and the D90, or the D90 and your wallet, I have not yet figured out.