The place where you install the stereo should be able to customize the center console for you to fit the after market stereo. Be careful though not to have some cheesy stereo shop to do the job, a friend of mine also owns an NSX and had an after market CD deck installed, the audio shop did a horrible job cutting the trim and taped with small pieces of black tape to cover the cracks, eww, that was ugly.
My friend has a shop in Redwood city called Auto Sound and Security. They did a 98 yellow NSX be4. I saw their job and I think they did a pretty good job. The other shop that do a very good job is Precision car stereo, but they are ridiculously expensive. I think you will be happy with Auto Sound and Security in Redwood city. Just tell them that you want a good job and ask for John. Tell him Andrie sent you.