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for now I can offer a fool-proof fix:
back up your device in itunes, then restore in itunes.
on the phone itself, set up as a new device and get into the phone. don't touch itunes yet.
perform the jailbreak (use evasi0n this time, do a proper untethered jailbreak), including the step on Luke's guide of opening Cydia for the first time to load the file system
open itunes again and restore from your backup to get everything back on your phone.
If for any reason you can't get into your phone, the above is always the safest route.