Wow, what a difference. Some time back I bought an air box cover for cleaning (pic below, keeps the air filter from getting all wet). One day, after washing, I checked my air box boot and there was a lot of water in there, enough that I was a little bit worried that some might have gotten in the carb. I dried it out and everything was fine.
After sealing my air box up with rtv and installing the Pro Seal gasket, I put the cover on and turned the airbox/subframe upside down (carb boot facing up) and filled it up with water. I only had a drop every second or so coming from the bolt hole of the No Toil cover, nothing else. So, I definitely had a big leak, which explains why I had a lot of dust and dirt past the filter.
Good maintenance move. Thanks for everyone's tips, advice and part numbers.