Are you riding through mud and water crossings??
Just curious as to why you are leaving the lid on??

 

Since the filter on the bike is stock and I live in the Desert if figured best to leave it on till i get my K&N pro flow.

 

If you are not riding in wet muddy conditions, I'd remove the lid.
If you leave the lid on, you are leaving horsepower on the table, as the airbox is one of the reasons why the YFZ is so restricted for air.

If you remove the lid, I'd go with a
45 pilot
Stock needle on the 5th to 6th clip position, or YZ needle on the 4th clip position
170-175 main

And adjust the fuel screw till it revvs clean from idle.

If you still insist on leaving the lid on, you will need to jet it a little leaner because you are starving the motor of air.