Have you vented the rear of the intercooler, i.e put a grill mesh on the inside of the wheel arch? this allow more air to travel through the cooler.
if you want to port/polish something you need to get the inlet manifold done, then the head and then the exhuast manifold. as doing one without the others is pointless really.
You will need to get the chip remapped after this work. What is the ISV re-route kit like, any good?