lol , its JimDirt , not JoeDirt lol
If your going to open up the airbox , i would first concentrate on getting it running good "as is" so as not to compound your issues , the more you do without sorting things out , the harder it will become to sort them out ... follow ??
IF you were to open the airbox , usually the main will remain the same (not always , but usually) , its the Main Jet that is affected by the airbox opening more than the pilot , since any adjustments can be made with the fuel screw for most compensation
Again , once you have it running "normally" with this setup , THEN you can start altering things , IF , while adjusting things in current configuration (with a new Pilot Jet) and you can turn the fuel screw out or in more than the specifications recommend , THEN is when you would change the pilot jet either up or down 1 size to compensate for the out of limit settings ....follow ??
As for filters , you dont want to Macgyver things like that , the one thing that is DEATH to these engines is DIRT , even a little slipping past a filter will eat your valves quicker than you can imagine , if you find even a slight amount of dust inside the air boot , it means your not sealed and dirt is entering the engine , yes even fine dust will kill the valves , its the most common issue why people have to prematurely replace valves , the airbox design (minus allowing more air by opening it up) is designed , as are the filters , to address this issue , and altering the intake tract by eliminating the air boot and airbox , will cause a expensive death to your engine
So cut the top .....YES , Remove the airbox , NO !
You should be around #40 Pilot and #130 Main Jet , and about 2 turns out on the Fuel Screw , any less than 1 turn out to run correctly , or more than 3 turns out would require the next jet size down/up
But search thru this and see what everyone else is running around your elevation
*note that some have modded airboxes , so take that into consideration , as it will usually change jetting from "stock" settings for the same elevation*