The quickest way to replacing system files that affect a major part of the look-and-feel is to use one of the transformation packs available. I've used Flyakite's pack before - it's easy to install or uninstall, and it makes the Aqua feel more complete.
You already seem to know about the various docks available, so that's one more aspect of it.
You can emulate the Finder bar of OS X with something like Stardock's ObjectBar, but I've personally never been a fan of either ObjectBar, or even the actual Finder bar in the Mac OS, for that matter. The Windows taskbar suits me much better as far as useability goes, but I threw that in as an alternative if you're into pixel-perfect UI emulation like some people are.
Finally, you have Samurize and other widget apps to add Konfabulator-like widgets to your desktop.
Of course, you now also have clones/lookalikes of lots of apps like the Finder, iCal, iChat, iPhoto etc.
Aqua-Soft should have everything you need, really, and
OSX-e has everything nicely organized.