No Valid Packages - and it Gets Worse

I used Version TrackerPro to update a few programs (Fission, GarageSale, Garmin Web Update, Google Earth, iBlog, Skype - and for some reason, my registered copy of SRS iWOW didn't survive an earlier update of iTunes).
THEN I tried to perform a differential backup with SuperDuper. It stopped working while trying to verify permissions.
My Applications/Library/Receipts folder is empty. My Macintosh HD/library/receipts file had ONLY the Install SRS iWOW.pkg file in it.
I begin to perspire lightly. It gets weirder.
I restored the /Receipts from last night's backup. Now DiskUtility verified permissions. All seemed OK. Until I went to open Keynote to edit a presentation I made. The program treated me like I was a new user, and asked for a serial number (or go ahead for 30 days).
THEN, after I opened the presentation file, I am greeted with an errormessage stating that TWO fonts are "missing."
I am going to stop doing anything else to the machine - how should I proceed? The only "important" new file that I don't want to loose is that presentation file...but I can save it elsewhere and fix the fonts.
WHAT SHOULD I DO NEXT? This is my first "real" system weirdness in my seven months of Mac ownership.
Clint Bradford
17" MacBook Pro Matte 2GB 09/2006 Mac OS X (10.4.9)

OK - An "archive and re-install" procedure performed by my local Mac Genius (Victoria Gardens, Ontario California Apple Store) got me back to darned near normal.
I lost a few registration files (EyeTV, FinalCutExpressHD, Garage Band's instrument folder, HyperEdit, iDVD, MacPilot, SohoNotes, Visage Login, Zinio Reader) - and my Canon iP90 Bluetooth Printer. But all info was readily available in old email messages or from Canon;s Web site.
Just an FYI: The install of iWOW SRS disappeared - and had to be re-run. But it is fine now.
What did I learn from all this? Probably to upgrade third party apps one at a time, and then verify the hard drive...and not to perform multiple upgrades of third party apps.
It'll probably never occur again. It was an interesting, illuminating exercise to go through all my apps one by one to check 'em out. I AppZapper'd 21 apps that I really was never going to access again...
THANK YOU for your assistance!
Clint Bradford
17" MacBook Pro Matte 2GB 09/2006 Mac OS X (10.4.9)

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