Loss of apps and major productivity due to 3.1.3 update

For some odd reason it took better than 12 hours to backup (I backup every few weeks using iTunes) before install of 1.3.1 (I have not jailbroken the phone). After completion, my massive, 10-page collection of apps were largely gone including some major productivity lost with the deletion of QuickOffice. iTunes now has a completely different assessment of my apps (listing less than half of what I had before starting OS update). Even Safari is missing.
The question is, how do I get back to my previous state with OS 3.1.2 and all of my previous apps and data intact (or are those irretrievably lost)? I've a feeling that a restore only puts it back into original purchase state and all apps will still be lost. Yes, I know that I can re-download at no cost, but its the fact that I have to remember all of the apps purchased and, more importantly, the lost productivity on my previous QuickOffice.
Am I out of luck here or is there a way to go back to previous state (not original purchase state)?

Apparently Apple got a lot of feedback from people that 'toggled' the "Image Tooltips" and couldn't figure out how to dismiss the cursor-tracking popup. It's now officially Cntrl-T. You can change it back or have it both ways by customizing the keyboard.
Aperture menu > Commands > Customize...
Tap the T key on the visual keyboard.
The lower right pane will show what's assigned.
Note that '^' (for the T key) is assigned "Image Tooltips".
If you drag "Image Tooltips" to the "No Modifier" slot it will offer to make a copy of the defaults.
Name the new set and modify it. It will appear in the menu you used to get 'here' as a Custom Command Set.

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