Recovering Data from iPad Stuck in Boot Loop upon Update to iOS 9
All relevant data is in /var/mobile/. You don't need anything from /. The Notes database in particular is located at /var/mobile/Library/Notes/notes.sqlite. Without knowing anything else about your situation, the most effective way for you to backup your data might be to just copy over the entire /var/mobile/ directory.

Also, only versions of iOS 9.1 and lower can be jailbroken at the time of writing. And no, you can't restore to iOS 9.1.

Another thing you could try is to go into Recovery Mode, backup with iTunes, update to the latest version of iOS while still in Recovery Mode, and then restore your iTunes backup.