Before you go hacking away, what benefit is the cone filter to you? Are you thinking you'll get better performance due to easier breathing, or do you just like the looks better?

If you're going for performance, I think you're heading the wrong way. If I understand correctly, you're going to mount the cone filter so that it sucks ambient air out of the engine compartment. The stock setup sucks air through a plenum from outside. Which air do you think is hotter? The air in the compartment.

Even a normally-aspirated engine benefits from denser air (though a turbo engine gets greater benefit), and suffers from less dense air. A good cone filter will allow more less-dense air into the engine, like giving a net effect of zero. If you mount it on a turbo, you're net effect is probably negative.

Before you get too far, have you considered trying the K&N replacement that fits the stock filter location? Do that and clean up the intake plenum to the airbox (or make sure that it's constricted as minimally as possible), and I suspect you'll end up better in the long run.

-cj