Trimming the air box
You need to trim the air box, not the air filter. If you mount the air box first you will not be able to install the lower cowl.
There should be a diagram (figure 9) with your air box kit that shows the approximate place where to trim the air box. "...Air box top plate must be aft of the scoop top to be able to lower the cowl straight down"
FYI, I ended up making a new mount plate to offset the air box to the right. The kit and directions as received resulted in very little clearance between the cowl and the edge of the air box. A few others have done this also.
Good luck.
Mike