How do you tune so that you maintain the handling characteristics of the car? I'm a bit different than some people here in that I don't exactly want to tune out imperfections but I do want to increase speed.
Transmission tuning, my friend. Tuning depends on the car, of course, but if you stretch gears you can minimize shift lag in the last 3 which are what will improve your lap times. Crash course in stretching/flipping your transmission:
Car with a minimum top speed slider of 99~110 - set final ratio to 1.500 above minimum, slide top speed all the way left, slide final ratio all the way left. Slide 4th, 5th, 6th gears all the way right, 1st gear all the way left, leave 2nd where it is(unless its a 5spd, then move it .050-.075 right of starting position), and move 3rd to 3/4 of the way to the right(this is the tricky one to get right, try to line up the gears so they make an upward line evenly). If you do this, each gear will start out within 1000 RPMs of peak horsepower, depending where you shift, and severely reduces shift lag.
Car with minimum top speed slider of 120~149 - set final ratio to .700-1.00 above minimum(higher top speed, slide it less), and repeat steps above.
It's not a foolproof system, you will have to tweak the final ratio you start with for certain tracks or horsepower limits, so you're not redlining in the straights or bogging in the low gears. AWDs also don't like 1st all the way left, they prefer starting position or further right, depending on horsepower.
This type of tuning doesn't affect the way your car handles on the track, but it does maximize your output of power.