Touche!
This is my thoughts on how to hook it up.
(I edited one of your pictures to show you - hope you dont mind!!)
Remove the items that have the word "remove this" on them from your car completely.
Connect tube 1 to either no.2 or no.4 (whichever is easier) with the piece of Silicone hose (the ft and a half long hose that came with it)
Then get some blanking plugs for the other 2 unused ports.
Connect the reducer to the throttle body and clamp with hose clamp
Fit Filter to other end
Enjoy the sound of mad vtax!
P.S. The pipe is only that hot cos it has coolant running through it for the IACV and it is metal so conducts heat.