These bikes need the airbox properly installed to run correctly.   Over the years I have experimented on the dyno by running them with no airbox and pod filters, versus heavily modified air boxes (swiss cheese lids) and basically nothing works as good as a mostly stock airbox with no more than about eight 1/2" sized holes drilled towards to the top of the airbox.

I haven't personally tried to do the K&N air filter hack mod which is very popular on the VTR250 forums and the reason I haven't is because in all my years of testing air filters, jetting carbs and tuning Fi I have found that the K&N filters more times than not actually hurt the performance of the bike rather than help it.

I wrote an article about my findings here:
http://www.rc51.org/airfilt.htm