Fredo,
I assume you're running an aftermarket ECU or interceptor to replace the AFM.
Cuh8er,
The box you refer to is the VSV solenoid. It purges petrol fumes from the canister into the plenum.
It won't affect your performance and I'm sure EPA would love to see it there (even if the hoses are blocked) as it is an integral part of the emissions system.
My advice would be use the charcoal canister (or one from another vehicle) as it will keep your engineer happy and the registration guys on your side.
I have one on my vehicle and it took a few minutes to run the tank breather line to it and connect it up. No one can say I don't have one.
Whilst your set up may not comply with the emissions standards it will look like it does.
The last thing you want is to be directed to an EPA test centre. This can see your vehicle off the road for a long time.