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Hopefully it was a bad connection or a connector that wasn't fully plugged in. However, it still could be a broken wire making an intermittent connection. After you get the ignition switch harness reconected, I sugest wiggling it while the key is in the "on" position. If the dash lights blink, you have a broken wire.
When replacing the fairing, I've found it easier to remove the fairing vents first and then pop them back in afterwards. It's realy difficult to get the vents aligned with the ducts while also aligning the fairing mounts.
That suggestion was made by Karl. Once it's running, wiggle every d** wire you can find. Right now I'm cooking brekfast, almost afraid to try to start Vinnie. I hope the battery is strong enough to do the job AND that I have power.