You just removed one of the best cold air intake systems made. Nothing short of a turbocharger or supercharger will be any benefit by taking up that space.
Don't do this!
That setup sucks up hot, turbulent air and causes strange problems with idle and low speed performance. It is a HOT AIR intake system!
I agree- an underhood cone style filter will result in fan wash and picking up all the under hood heat. If you want to replace the factory CAI then at least go with an aftermarket fenderwell CAI- I have one but have to admit the gains are probaly minimal- 10hp . Most people do it for the look.
If you have the factory silencer in the fenderwell- remove that. You can also put a K&N filter in the factory airbox and pick up a few hp.
You'll need to get creative and make a panel to cover that hole. I made one for mine out of black phenolic plastic. I mounted my MSD box over the hole on my SSC.
Here's what I came up with. Its held on with double sided 3M tape