My own instinct is that after I did the original 10.4.11 Combo Update, then downloaded a fresh copy of Safari 2 and began using it, that Safari 2 altered some files that were essential for Safari 3, so that Safari 3 can't access them anymore. (Although that doesn't explain why I was unable to use Safari 3 after reinstalling it. Perhaps the reinstall failed to alter the files back.)
Now I understand the problem. And it's not "minor". Safari 2 and Safari 3 are very different applications. Each integrates with other Apple applications (Mail, iTunes, iChat etc). Your actions have complicated/compromised the OS, which may lead to other problems as you continue to use the computer. 10.4.11 is designed to run Safari 3, not 2.
As I suggested in the previous post, best approach is to reinstall the OS. Archive/Install will preserve your present settings, plus create a new folder called "Previous Systems Folder". Inside, you'll find your 3rd party Library items, which you can move to the newly created Libraries. The remainder of the files in that folder can be trashed. If you haven't done so, read the linked article about A/I. Also, if you rather use Safari 2, then after the reinstall, only upgrade to 10.4.10, using
this update.
Let me know how you make out.