After I jailbreak, I will want to back up the entire file system, What are some recommended tools? Can I install an ftp server, log in form my pc and get everything?

For stock iPad stuff, use iTunes to back up the iPad. For jail break tweaks and settings, I use PKGBackup (~$7.99, USD). It's a great program that I've used many times to put my iPad back the way it was. You can save your backups on the iPad or in the cloud (Dropbox). There are others but this is the one I use.

Between these two programs, iTunes and PKGBacup, I've been successfully running my iPad for over a year and a half. Havent lost anything yet (knock on wood).

Of course, and as always, YMMV. Good luck.

Marilyn