I decided to delete my VM disk and go back to before I patched all the binaries, and do each patch one at a time. Apparently, what broke it was an AMD-specific 10.6.4 dynd patcher I downloaded. It seemed like a good idea at the time I suppose.

I was able to run the binary patches using Marvin's AMD tool, so now most of things I was having trouble with are now all fine: AppleScript, logging in/out, Keychain (Mail doesn't even require tweaking, oddly enough). The console is amazingly quiet, with minor complaints that are either normal for osx86 or running in VMWare.

Sorry to jump the gun on posting about this, but I hope this helps someone else in the future.