Starting All Over With OS X and Safari After Update And Crashes

I had posted my troubles in the Safari Section under the same title and got fabulous advice. I was just starting the process of following this advice so that I could get my mac back up from 10.4.7 to 10.4.11 since the genius' at the bar at Apple had re-installed the OS to fix the crashing Safari, Mail and Software update apps.
The advice suggested starting with a permissions repair and a disk verify. Well disk verify may well have come up with the cause for my computer going foobar upon installing the last Apple update in the first place. (Incredible that the Genius Bar guys missed this, especially the week before when I had taken my Mac Mini in for a Procare "Tune-Up." I wonder what the H-E Double Hockey Sticks they did if they didn't verify the disk in the tune-up? Wouldn't that have saved me all manner of distress and trouble!) Here is what verify gave me:
Verifying volume “Macintosh HD”
Checking HFS Plus volume.
Checking Extents Overflow file.
Checking Catalog file.
Invalid index key
The volume Macintosh HD needs to be repaired.
Error: The underlying task reported failure on exit
1 HFS volume checked
Volume needs repair
So..I will need to, if I understand this correctly, re-start from my install disc holding down the C key and then go to disk utility. I have never done this before and really would like some one to walk me through the procedure.
Just to remind or get you up to speed. I have a mac mini that had been bought with 10.3.7 on it and had been updated all the way to 10.4.11 and Safari 3.0.4 but after the last Java, Quicktime, and Security update Safari, Mail, and Software Update all crashed repeatedly. Genius Bar at Apple got them working again by re-installing the OS but put in 10.4.7 and with it Safari 2.0.4. Now I will need to repair the start up disk. Do I use the Mac Mini "Mac OS X install disc 1 and Apple Hardware Test" disc or do I use the "Mac OS X Tiger" disc that I bought to upgrade my Mac from Panther to Tiger? I think the former rather than the latter but I am uncertain and would really like to know exactly what I need to do before proceeding. Please help!
Then.. what do I do after I re-start using the install disc and have gone to Disk Utility. Will it then darken the "repair" button under "disk," and allow me to click on that to repair the disk? What will that do to the applications and documents that I have in the mac. I actually have my iTunes and iPhoto libraries on external hard drives and are backed-up on yet another external hard drive. I think everything is backed-up. I will perform another back-up before I do anything anyway. Do I leave the externals on and connected while doing the re-start using the install disc or do I disconnect them?
As you can tell, this makes me rather nervous. Thank you so much for any help you can offer! -Charlotte

Hi. Sorry for the delay in responding; Holidays as you know. Anyway... Thanks for your advice.
Yes, I put in the Tiger install disc and holding the c key restarted the computer. Went to Disk Utility and ran Repair Disk. Did it twice as you suggested. The first time it said that there was nothing to repair which was a complete surprise. Ran the verify again and ran Repair Disk again. Each time the report shows no problems. After booting back into the main internal hard drive, I ran disk verify again and it reports no problems.
Someone else on a different post on this subject (I accidently posted this in two different places) stated that the Apple Disk Utility Repair would not be able to make this repair and I would have to get Disk Warrior to make the repair. If Disk Verify reports no problems, wouldn't this mean that running the Repair Disk did repair it?
After all this I went to Apple's site and got the combo update and ran Software Update and gotten my little ppc Mac Mini back up to 10.4.11 and Safari 3.0.4. (I ran permissions repair after the updates as well.) I did not, however, download the last Security Update, as some posters have suggested that I avoid it. What do you think of the Security Update 2007-009? Would this be safe to download and install, now that my mac seems to have had it's directory repaired? Thanks so much. -Charlotte

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