Jailbroken iPad stuck at boot screen and looping
The obvious answer is to re-install the OS and then ssh in to run fsck.

Have you looked into a program like PhoneView that will let you mount iOS device as an external drive and use Disk Utility (if you have a Mac) or fsck? The FAQ for PhoneView has a windows software recommendation that does about the same things if you prefer that OS on the desktop.

(edit: I don't know of any free alternatives that mount the file system)