Well i usually just buy the parts in the order they appear in the tuning-shop menu's (i.e Exhaust, then Brakes, then Engine, etc)
Then test the car out as it is with those parts, and takes notes on what i need to adjust, reduce, increase, etc
Then give it that basic tune, test it again, and then focus on 1 part at a time 'till each one is fine-tuned
But i haven't tuned a car that in-depth for a while now, most of the car's i drive now handle good as they are (stock RX-7's, etc), and if not i've just dealed with it and driven them the best i could make them