I assume it got knocked over on to its right side.  Based on your description of the air filter, it sounds like oil may have run through your breather into the airbox.  How long was it on its side?

It's also possible that you already had a heavy accumulation of oil in your airbox.  That accumulation would have been collected in the bottom of the airbox.  When the bike got upended, the oil would have run to the right side of the airbox and started seeping into the paper filter element.  That would have acted like a sponge and drawn the oil up into the pleats.

Take the filter element out and ride the bike.  Only a brief ride, diagnostic only.  See if it corrects the way your engine is running.  Don't continue operation without the filter, just a brief diagnostic test to see what you can learn.

If the spill tweaked your muffler, there's a good chance you have an exhaust leak too.  Exhaust leaks exacerbate the backfire phenomenon.

Thank you for the responses --

I made this origional post while at work, and on the way home (About a mile) The bike was extremely sluggish -- when i got home, I noticed the head pipe, like 12 inches past the connection to to the head, was RED HOT.

I'm guessing there is absolutely a leak somewhere? What do you think?

How much damage have I done?

... wondering if I can get an insurance claim for repairs, might be in over my head.  

Thanks everyone.