I would leave the bottom on the airbox, because you get much colder air with it still there. If you take the resonator out of the wheelwell, I don't think the rubber joint from the airbox to the fender is that bad of a restriction, given the size of the throttle body and MAF. (Maybe it is, though. Jamming some kind of cylinder in it to stretch the rubber might help...)
I may try your idea of the cylinder later.
http://www.contour.org/cgi-ubb/ultimatebb.cgi?ubb=get_topic&f=1&t=012178 These cars are great, I just wish I had known earlier!
Stephen