Corrupt Library - how to resync iPhone & iPad

My iTunes library is corrupt - I have some issues with podcasts not being deleted properly.
I know how to rebuild my library via the Apple Knowledge base article http://support.apple.com/kb/ht1451.
I know that that works and solves my issue. All my content is safe and is, after a bit of tweaking (podcasts must be resubscribed, iBooks relinked, apps transferred from iPhone, etc.), seen by iTunes.
But, and this is a major problem for me, it looks like after rebuilding my library, my iPhone, iPad, iPod Nano, and iPod Shuffle all think they are connecting to a new library and only offer to erase and resync.
That said, I have a few questions:
1. I know I can transfer all my apps from my iPhone to iTunes. But what about app data. I'm assuming that will all be lost. Is that correct?
2. Is an erase and resync my only option? I literally have hundreds of apps on my iPhone and several dozen on my iPad. Many of the apps contain important data and settings. Further, each device has many, many settings (email servers, passwords, wi-fi passwords, VPN settings etc.) and are setup exactly the way I like them. My only option is to start over from scratch?
I have the iTunes generated backups of each device. After I rebuild my library, is a restore of some kind possible? It didn't appear to be when I looked on a test run.
Thanks for your help.

vbeachcomber,
If you copied the entire iTunes folder in My Music over from the previous install your playlists should have been retained. There is no way to sync playlists back from the iPhone, but you can transfer purchased music if the computer has been authorized for your account.
Did your Windows XP Pro install disc come from a computer that included a web camera?
Regardless, our buddy Roy would probably want to see the Minidump file that should be created when you get a Blue Screen. Here are the steps to make sure the file is created:
1. Right click on "My Computer"
2. Select "Properties"
3. Select the "Advanced" tab
4. Select the "Startup and Recovery" Settings button
5. Select "small memory dump" from the popup.
Reproduce the Blue Screen. After the computer blue screens and restarts, look for
the MiniDump file. The original properties dialog where you set it up
to collect the minidump should tell you where the file will be
saved. It's usually in the folder "C:\WINDOWS\Minidump" and is
called something like Mini<number>-<number>.dmp.
Attach the file to an email, along with a link to this thread and send an email to Roy.
Be sure to include the following information:
A link to the thread on Apple Discussions where your issue is being discussed
The username you are using in the thread
The version of iTunes you are using or trying to use
A concise description of the issue you are seeing
The exact text of the error message you are seeing (if you are seeing one). In this situation a Blue Screen.
If you are sending in log or crashdump files, Roy will need the files themselves, not just the text of the file pasted into the email.
Thank you,
Nathan C.

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