I believe the "pre filter' on Knight's bike is just that. Not meant to replace the original, only supplement it by slowing down mud and water splashes.
I have the same water buildup in the airbox even when just washing the bike. I don't know if it will help but i took out the bleeder valve and slotted it much more with a knife. It is just like the mouthpiece on a Camelback, I slot them out too so they will flow better.
Motocross bikes frequently cut round holes in the airbox to let in more air for power and cover them with a screen. You could always try it with the sidecover off to see if it helps power. By the dust pattern on the filter it is obvious that the air is primarily coming from one small spot which is bad for power and also filter life.
I also found both of the round seat to frame bumpers had come off the seat base and were in the bottom of the airbox after this weekends MX race?