Iphone won't sync properly after iOS4.0.1

Hi,
I'm writing here after searching the web and Apple and finding no clue on what's going on
I recently updated my iPhone 3GS to iOS4.0.1 and as a prerequisite I had to upgrade Itunes to 9.2.1.5.
After upgrading both my iPhone OS and Itunes I can't sync anymore!
I can't sync my Contacts/Calendar/Apps/Music/Podcast etc...
I keep getting errors like:
1. Duplicate file name
2. Device timed out
3. can't write to disk
4. File can not be found
Solutions I've tried:
1. Running Diagnostics via iTunes showed everything is working fine.
2. Removed Apple USB controller and re-installed.
3. Made a complete remove of iTunes + QuickTime + Apple software + Apple Mobile and reinstalled iTunes.
4. Did over 20 Restores!!!
5. On the Iphone chose to "erase" everything.
6. on the Info tab, unchecked "Sync Notes".
7. Removing any of iTunes music folders.
Nothing worked! I have a working phone, which I should be grateful for, but I can't sync my music, podcasts or my NIKE runs. I can't even downgrade back to 3.1.3 because it says Apple won't sign the firmware!
I heard that if I "Jailbreak" my device I can downgrade, but I don't want to void my warranty or harm my device.
Can someone please help me?

Try turning your security software off - my laptop running Windows7 and Norton 360 was able to download the iTunes upgrade and work with my iPhone and iPad, whereas my Vista laptop with ZoneAlarm has never let me do an iPhone OS update with ZoneAlarm on, so I turn it off for OS updates. No need to turn it off for synchs after a successful OS update. Btw, I still have not been able to update iTunes on the Vista laptop no matter what I do (turn ZoneAlarm off, download only followed by manual installation of update, etc). Hope this helps!

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