Ok. It looks like all this work was for pretty much nothing. New solution is in order:
Step 1: Update our Bukkit to the latest recommended build, it's either R6 or R7 right now.
Step 2: Update mcmmo to build 1.3.02
Step 3: Upload the old backup with all 1,274,339 bytes in all its glory of hugeness.
Step 4: Cry.
Step 5: Use the new /remove command in mcmmo v1.3.xx to delete all 0EXP 0Level players from that file.
Step 6: Pray.
Step 7: Reimburse all new players as best I can with mmoedited stats to compensate for the fact that they didn't exist when the backup was created.
Step 8: Cry more.
As soon as the admins ok this course of action, and the server population is low enough to not disturb too many with the downtime, I'll go through with this. Thank you all for being so patient and calm (well most of you. Others just bugged the fucking shit out of me and I want your stats and mcmmo access removed forever. But I have more self control than that.) during this setback in our history. Let's hope the next one (there will be more problems, such is the way of minecraft + human error) is far away, and not nearly so prolonged.
