A picture would help!! Are talking about the helmholtz resonator for making the intake quiet? I would use the connection for the crankcase breather onthe new filter or else the unburnt fuel and acids and other crap might just sit in the motor and then condense back on your valvetrain and eat it up, You could leave the filler cap but at least hook up the one to suction out the bad stuff. What are planning on using to connect to the plenum to air filter? The thicker the material the better to prevent heating upthe intake air. If you could run it inside another pipe even to insulate it will
help. I would use some sort of barrier to keep engine heat away from the filter and use some dryer duct to bring cold air to the filter area, I have some in the bottom opening of my grille then it drops down a bit so water can settle there and drain out of small hole, then it goes up and is about 4 inches away from the stock filter box opening, Just to get some high pressure air to it but not bring all the junk directlyto the filter.