Wheels look fantastic mate
The 3mm you wish to remove; is that because you you have zero clearance (wheel will turn but has a bees dick of clearance) or -3mm (caliper is fouling on wheel by 3mm)? You are going to want at least 3-5mm spoke to caliper clearance; just in case you catch a small stone; it'll trash the front of the caliper, and the back of your nice new wheels.
You'll be safe with taking the script off the calipers, but I wouldn't be going further than 1mm unless you are prepared to pop the pistons out and actually measure the material thickness on the front face.
Either that or look towards Pipster's find; 350Z/ Murano twin piston 325mm budget upgrade, the s2 G35's in the states run this same setup.
Link; http://www.skylinesaustralia.com/forums/topic/82083-stagea-brakes/page__pid__5989328__st__920#entry5989328