The updates don't exactly matter above iOS 6.0.2 for the iPhone 5. 6.1.4 fixes a speaker/sound bug, but I don't see a difference at all. To wipe your jailbreak data, use ILEX RAT to do so, it'll revert it back to a freshly jailbroken stage.
http://www.iphoneforums.net/forum/iphone-jailbreaking-17/wiping-all-cydia-tweaks-without-restoring-rejailbreaking-56461/
As for your stock user data, you'll have to manually delete those.