Bob,
At the very least you should have downloaded the Combo Upate (165 MB) at the link below, assuming you are only using a PPC Mac:
http://www.apple.com/support/downloads/macosx10410comboupdateppc.html
I am under the impression that once you update to more higher versions than on the Install Disk, that you only have two choice of reinstalling, and they do not include Upgrade -- see:
http://docs.info.apple.com/article.html?artnum=301270
In particular the note that reads: "Note: If you've updated Mac OS X 10.4 or 10.5 to a later version than what is on your Install disc, you can't use this option, but you can use others described below."
I am well aware that when doing a custom install of individual applications from the Install disk, the Combo Update must be used, and not Software Update. Otherwise you get the application out of sync with the rest of the OSX. I think this may have gotten you into trouble, and I don't know exactly where you are.
If you were to redo an install, then as far as Mail, you would only need the com.apple.mail.plist file from Home/Library/Preferences, and the Mail folder itself (Home/Library/Mail backed up and replaced when the new installation is stable.
Ernie