There are third party programs to backup your iPad. I don't use one, so I can't recommend any. Daltonbaker provided a link to several a couple posts back, but from the context I'm not sure if he has used or is actually recommending any of them.

iTunes is an all or nothing restore, and it only restores app data, contacts, and other stuff (books, music, apps, video) visible in the iTunes library is synced, not part of the backup itself).

Here is the best source of info I could find about backups in iTunes. It will tell you most of what you want, though it might take a bit of digging.

iPad: About backups

The Commodore 128 had a CP/M mode. I fiddled with a it a bit, but never had the ambition to dig into what it could do.

Bit the bullet and used iTunes to delete the backup - it cleaned out the folder! 1,391 files gone - poof!

Did a sync:
Step 1 - Backup phase: 12 minutes; 1,403 files, 9.89gb
Balance of sync: 2 more minutes

Result of exercise - same amount of space used on hard drive; all new files!

Glad it worked for you.