Intercooler should be getting air from a pvc pipe under the car feeding up and out a cos worth vent in the bonnet. That's how it was set up when I had it.
Mine was dead stock, with whatever pads were in it, and 205 dunlop semi slicks. Would lock the inside rear going into corners but that was more from the unweighting of the rear. Climberjoel had upgraded replacement rotors and pads and toyo r1r. Not sure what the weakness of his setup was but...
Why brakes AND tyres if the tyres do all the work? Stock brakes were fine on my micra at wakefield and I'm pretty sure Climberjoel had stock brakes on his....
Swaybars, 2nd hand coilovers, panhard rod, wider wheels and good tyres. IMO don't bother with engine performance mods.
Oh and power steering if you don't already have it.
It was a couple of years ago when I did it, but at the time you could download a 1 use version of the software for free off their website. Then if you wanted to tune again just delete it and download it again :)