Tracking down culprit file

I have a problem, already posted in the GB and SL forums here, concerning a missing Glossary in GB '11 in the Admin account on my iMac.
The Glossary is available, though, in a new User account I created specifically as part of my troubleshooting.
I'm on a mission now to track down the cause of the problem in the Admin account. I'm making the assumption that ~/Library/Preferences is a good place to start looking.
I have a list of the files in the User Preferences folder, and am comparing it with the one in the Admin Preferences folder.
My intention is to remove, one at a time, any files that are in the Admin Prefs folder but are not in the User Prefs folder in order to check and catch the offender. I also intend to put back any removed files that don't seem to be causing the problem.
Do I have to do anything in particular, such as quitting GB, restarting or logging out and back in, before reopening GB?
I've run AppleJack and DiskWarrior (both up to date versions) on the iMac and still have the problem.
I'm prepared for the long haul.

Starting with a list of what's working in the new account, you log into the old account, move everything to the desktop folder, log out and back in. Launch GB and see if the Glossary's available. If not, then there's no sense proceeding because something else is amiss. In that case, you might want to try the second way:
While logged into the newly created admin account, backup the bad account's folder, delete the bad account, selecting the save data option (which is stored in /Users/Deleted Users/ as a disk image), recreate the bad account using the same username/password combo, log out and back into the recreated original account. If the problem's solved, open the saved data dmg file in /Users/Deleted Users/, open the /Library/Preferences/ folder from the saved data, open the current /Users/restored account/Library/Preferences/ folder, and slowly copy plist files from the saved data folder to the current one that don't exist in it. Log out and back in to ensure there's no conflict and things still work correctly. Resolving conflicts or identifying corrupt plist files is a laborious process. Good luck.

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    Location: /System/Library/Extensions/PatchedAppleNVRAM.kext
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    Valid: Yes
    Authentic: Yes
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    OpenPMUNVRAMController:
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    GossamerDeviceTreeUpdater:
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    Valid: Yes
    Authentic: Yes
    Dependencies: Incomplete
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    that is the list of extensions that are reporting some sort of errors. at first i was figuring it was a problem with the driver for the Pioneer drive but my friend brought over his digital audio G4 which was also running 10.4.8. and we decided to try the drive in his Mac to see if there was any problems. it mounted everything we threw in it. it played dvd's great and played audio cd's great, it copied files over to the hdd without fail. it even burned a flawless cd. ok now the ideal of the driver for the drive was thrown out the window. so it has to be something else causing the problem. either a driver for a part on the motherboard or what i have no clue.
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    yea i have along time ago and also made a update to xlr8's drive database. cause i fixed the problems with the drive in OS 9.2.2 (AKA no burn support with the built in burning app or iTunes, now have full support for burning with the finder burn and iTunes thanks to a edited PioneerCDR authoring support extension that someone edited for me. found out that the Apple CD/DVD driver extension was at fault for the locking up on wake up with hdd sleep enabled that started when i installed the Pioneer drive. fixed with intech CD/DVD speedtools 6.0).
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