Troubleshooting -- rich carb? UPDATED 8/16/10 5:30p

[ruxpin76]

So....bike ran like a top for most of the past 1500 miles. Regular oil changes, only difference was drilling out pilot jet cover and running the pilot/idle screw at around 2 turns.
About 100 mi. ago, bike developed a condition where it would kinda' bog/hesitate on acceleration until warm, then run great. Occassionally it would seem to "surge" if held at constant throttle grip position.
This seemed to get a tad worse, and then 2 days ago I made the mistake of checking my air cleaner. Discovered inside was gunked up a bit, and wondered if that was the issue. Drained/cleaned the bottom of airbox and washed the air filter (had to order a new one, none local). Let air filter dry, reinstalled. Removed spark plug and used emory cloth to polish electrodes (appearance was light tan/whitish on insulator)

Reinstalled plug and air filter (seemed dry...)

Went for ride and got 2 mi. before bike just died and refused to crank. Removed air filter and there was 2" fuel in bottom of airbox. After draining, and left for 2 hrs. bike cranked.

Filter was soaked, so I pitched it, and managed to ride the bike back home the next day (2 mi.) without the filter. Wasn't "crisp" on throttle, but ran "OK".

Soooo....any thoughts on what caused all this? I'll have the new filter to replace on Tues. and will try it, as well as a brand new plug. Bike ran great before this, and hoping it's nothing major. Will have the carb removed and rejetted next week too.

Cheers,
~Ted