Personal opinion - you wasted your money unless you are racing and need extra top end.
Running with the air box lid off and the K&N filter are for top end performance enhancement. Modifications for top end come at the cost of low end. You can get rid of the bog by enrichening the air/fuel mixture on the low end. This is what happened when you put the air box lid back on. It increased the restriction to intake and slowed down the velocity of air passing through the carb allowing the passing air more time to pick up the fuel necessary to make the engine perform acceptably.
If you ride primarily on a MX track, increase the size of the pilot jet by one size and adjust the fuel screw for an acceptable idle. This might improve the low end.
If you ride in primarily dusty conditions, throw away the K&N filter (they pass more air, but they also pass more dirt and they need to be cleaned and re-oiled after every race), put the stock filter in and leave the top on the air box.
Just putting on the header will increase low end power, but the re-jetting is only necessary after riding it to see if it needs rejetting.
Another thing that will affect a bog on the low end is how the accelerator pump is adjusted or working. If the pump does not shoot gas down the throat of the carb immediately at the throttle is operated. a bog will occur.
Good luck
Running with the air box lid off and the K&N filter are for top end performance enhancement. Modifications for top end come at the cost of low end. You can get rid of the bog by enrichening the air/fuel mixture on the low end. This is what happened when you put the air box lid back on. It increased the restriction to intake and slowed down the velocity of air passing through the carb allowing the passing air more time to pick up the fuel necessary to make the engine perform acceptably.
If you ride primarily on a MX track, increase the size of the pilot jet by one size and adjust the fuel screw for an acceptable idle. This might improve the low end.
If you ride in primarily dusty conditions, throw away the K&N filter (they pass more air, but they also pass more dirt and they need to be cleaned and re-oiled after every race), put the stock filter in and leave the top on the air box.
Just putting on the header will increase low end power, but the re-jetting is only necessary after riding it to see if it needs rejetting.
Another thing that will affect a bog on the low end is how the accelerator pump is adjusted or working. If the pump does not shoot gas down the throat of the carb immediately at the throttle is operated. a bog will occur.
Good luck