Software updates- Security&safari 3.1 update... does not boot

hi everyone,
i'm trying to help my room mate out with a problem. he has a mac mini intel 1.66ghz. he does have 2gb ram installed by a apple certified tech a month ago and it is problem free.
here's the dirty stuff. so first off, he has a western digital My book home edition 320gb usb/fire external with his files on it. when he restarted his computer after coming back home for the weekend, the error came up that that went system error, and it could not find certain files related to the mybook. it almost seems like the data was corrupted or deleted, he did not move or touch any files with the hard drive. i know there have been issues with the quality and hard drives failing particularly my books.
so the computer worked we tried to unplug ang plug back in the HD. also restarted the computer.
he had to also reinstall office 04, that went fine and worked. we also noticed that the printer he had connected could not be found, in sys. pref. we could not add the printer to the preferred list and it was searching for drivers on the bottom with a grey spinning wheel.
we gave up on trying to work on those two problems. he was working on a worpad doc and a powerpoint. finished, saved, and then installed the security updates for safari (3.1) and also i believe the 3/18 security update. we did the needed restart and then the mac got stuck on the grey apple boot screen with the spinning grey wheel.
we ran the disk utility, verified, there was a problem it was an incorrect volume, or piece on the internal HD(can't remember what the exact error on the HD was) so repaired it and it said it was ok. ran a verification again and it said it was ok.
so we try the restart and the screen is still stuck on the grey/apple logo/ spinning wheel.
...help!
so could this be an issue with the software update? is it the problem with the disk repair? we ran it a few times to verify and it said ok each time. we did not verify permissions...dont know if thats possible in the DU on the tiger cd.

First item: You should always repair permissions and verify (and if necessary repair by booting from another drive and using Disk Utility) any volume before doing updates. Also repair permissions after doing an update. Finally, I always clone (100% bootable backup) my drive before running any updater just in case something doesn't work.
I'm not expert enough to tell you what those extensions do, but I'd guess that because you didn't run the updater on a properly repaired drive that something didn't get installed properly and that's what's giving you trouble. In that case re-running the installer on the now hopefully repaired drive might work to install those components correctly. Again, remember to repair permissions before and after.

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