I had to do everything MANUALLY. I read somewhere that it happens when the media you are transferring from device to the PC is LARGE. Since I had 20 GB of stuff to transfer/backup, iTunes would freeze.
What I did was:
1. I took screen shots of each one of my home pages with the folders open. You can probably do that with your music folders, too, I'm not too sure but you can try. And since you're jailbroken, take screen shots of your tweaks and extensions, too, or write them down on a notepad.
1a. Make sure you copy/paste the screen shots to your computer. Even if it doesn't sync, your iPad still shows up as a drive, so you can copy/paste from windows explorer.
2. I deleted the apps MANUALLY, at least to a size that is small enough for the ERASE ALL CONTENT AND SETTINGS on your device. I found out that if the file is still large, it takes a longer time to finish, and it would seem like my iPad has hung up on me. So, better to really reduce the size of your media content.
3. At this point, make sure that everything you can backup manually is backup-ed. Like, things you can backup to iCloud or Dropbox, do it now. Open your games and back them up to Game Center.
3a. I also tried to transfer purchases at this point, thinking it might be small enough already for iTunes to handle, but I still failed.
4. Next step requires you to be brave, it is to ERASE ALL CONTENT AND SETTINGS. I used that one instead of the other RESET buttons.
5. Once your device has completely reset, it will ask you for the usual things like, what language you will use, etc. When you get to the part where it asks you if you would want to set up your device as a NEW iPAD or backup/restore, choose backup. Mine is connected to my laptop via USB cable the whole time so when that part comes, I see on my iTunes that you can choose to backup from a restore point. Choose that one and it will give you backup times you can restore to. Choose the latest one.
6. Miraculously, all my calendars, contacts, etc were actually backup-ed by iTunes even if it looked like it froze, so I was pleasantly surprised to see them restored to my iPad. My iPad has no apps and games but when I re-installed them, i.e. Plants vs. Zombies, my profiles were actually saved as well.
7. Manually re-install your apps based on the screen shots you took, or have an entirely new one. Now's your chance to finally be rid of apps you don't really use so re-install only your must-have apps like I did. But that's totally up to you, of course. Then try to slowly "break in" your iTunes. Install a few apps and then transfer purchases (make sure that you allow iTunes to do this by clicking on the Apps tab and checking the box that says Sync Apps), install again and sync, install and sync.
8. If you want to jailbreak your device, you can now do so. Just make sure you have no more problems with iTunes anymore before you do because jailbreaking can have different issues you might encounter.
There you have it. I had to devote a whole afternoon to it. Depends on how much you have on your iPad. You might probably have to devote the whole day for it. It's a lot of work but hey, as long as everything works from now on, that is tons better than not being able to backup to iTunes.
Good luck, my friend, and tell us how it went from your end. *hugs*