Did you plug off the line going into the airbox?
Yes I did.
One more thing is that I did take a hose and clean off the top of the engine, but I did ride it a mile or two after that, so i would think any water that would or could of caused the problem would of dry-ed up.
OK, just checking for the obvious stuff. Haven't followed the thread on these block off plates, I assume you used some sort of make a gasket goop to install them?
There are some connectors on top of the motor that are not watertight, in particuler the red and white connectors for the ignition switch come to mind. If you haven't done this I would disconnect them dry 'em out and add a generous amount of dielectric grease. Even without the hose these two connectors are exposed - you can see them from the front of the bike underneath the fairing if you look closely.
Might also be time to pull some plug wires and make sure everything is dry.