The intake chuff is normal, you usually don't hear it with the stock intake though.

Somehow my 08 speedo is water tight...might be because I sealed it on the back side of the "trim ring" with RTV though.

Shitstain from the timer cover? There isn't anything to leak from it...explain?

So far mine hasn't leaked a DROP from anywhere other than occasional "wet" clutch cable right where it comes out of the derby cover, but it's only about 1/2" down and never gets much worse. The whole bike stays clean except for the damn bugs and road grime.

Did one of your A/C bracket screws get ingested somehow? Did you have them off at any point or just came loose from factory? It's been a while since I removed my stocker so I don't recall exactly how it's setup, but I'm surprised it was able to make it past the filter.