I've got the 9" K&N, and my PCM in there also, and I can get the pump to fit. It will take a bit of coaxing to get it to mount solidly, but has anybody else actually put the pump in the airbox? My only concern is that it will partly block the airflow that would come in through the headlight hole.
I'll have to play with it later this week to see if I can figure something else out.