Restore your device, but do not restore from a backup. there WILL be lingering jailbreak-related files in your backup from within iTunes that will take up space. I noticed this after I restored my iPhone 4 two years ago, then rejailbroke it and only installed iFile (i believe that was the name) and noticed that a lot of my winterboard themes were still on my iP4. I never reinstalled any of these themes after i rejailbroke, and i did a full DFU restore with iTunes.
Doing a clean restore without using a backup gave me a proper, clean install of iOS and the file system.