Welcome and sounds like a couple things can be done to get rid of the minor annoyances.
WRT the rattle, at least the hatch rattle. I can be adjusted at the latch and it will cure that nasty noise. There is a thread on here with a couple ways to fix it.
WRT the windows / air noises. Yup, especially in crosswinds. An easy fix is turn up the stereo. Other things that may help are: new weather stripping, window adjustments, treat the old weather strippings to soften them up.
The knocking noise you hear may be something different than what is commonly heard / referred to as knocking at low idle by most folks, but it it is the common noise, it's the fuel injectors. They all do it, some more so than others. I don't usually hear mine unless the hood is open / and or I'm outside the car though. If you here it inside the car, it could be something else. May want to see if fuel injector system cleaning may quiet it down. I have a lot less miles on my 04 than yours too, so it could be something else.
The head gaskets do leak and the simple fix is, replace them. Not expensive or to time consuming if you do them yourself.
Good luck and post us as your ownership continues.
Hi, and thank you for the tips.
I forgot to mention that I also used that Chevron Techtron stuff you add to the fuel. I also added a quart of Marvel Mystery Oil during oil change as some have sworn it helped with engine knock.
What is everyone's idle speed? Mine is at that first bigger mark ~ 500rpm.