The second small K&N style filter was for the IAC port, but I believe there is an update to that from Full Power Perfromance and I don't think it used anymore? Call FPP...
The T in the sense line for the controller is for a boost gauge, cap it if not using one.
The connector is for your airbox temp sensor, you need to remove the sensor from your old airbox and keep it plugged in so you don't get a code, ziptie it off to something so it doesn't flop around. The sensor is NOT used in the new intercooler airbox as it is not designed for postitive pressure and will blow out.
The small line is a vent line, I am not sure but call FPP.
That is an awesome kit.
Mory