I don't see how the ABS pump causes warped rotors in your scenario...or any scenario for that matter. It doesn't make pressure...the hydro-boost and master cylinder make the pressure for the system, and the ABS pump modulates it to enhance braking in certain situations.

Are your brake shields all intact? What kind of brake lines are you using, and how old? How often are you flushing/bleeding the brake fluid, and to what extent? Complete replacement or just rotating out fluid from the caliper chambers?

I've not had a warped rotor yet, but I have had problems with slide pins (my own dumb fault - too much grease) and caliper pistons sticking.

 

I've never had a warped rotor either, and the majority of EX's my miles are heavy towing (although the trailer takes care of it's own braking needs the Ex does work harder in "panic stop" situations).
How abusive are you on your brakes? Not busting your stones, its just that some folks tend to be very hard brakers as compared to those like me that tend to be easier on the pedal. And of course the dreaded two footed drivers that rest a left foot on the pedal sometimes, those drivers can really heat up a set of brakes doing that.
The Wilwood setup you are using, does it require the 20" wheels for clearance over the larger brakes? The ones I have seen do look like a sweet (but pricey) upgrade.
Another thing to consider, not all "warped rotors" are in fact warped. Sometimes it is actually an accumulation of brake pad material (I think it termed "cementite") transferred onto/into the rotor which happens after a hard (very hot) braking event where the vehicle sits still with the brakes still firmly applied. The heat allows some small bits of the pad material to bond/blend with the rotor face, a combination of the high heat and applied pressure. This spot of transferred material will, under braking feel like a warped rotor as it will give a pulsing feel due to the differing friction between the clean rotor areas and the spots of transferred material. One way to help avoid this is to gently "creep" forward after a hard stop, only a few inches of rolling will keep any single spot of the rotor from seeing the steady heat and pressure. It's a habit that I have ben using for years on all of my vehicles and I have never had any type of "warped rotor" issues and I get pretty long pad life too.

 

 

The pressure in the brake system comes from you pressing the brake pedal only. The hydroboost unit is a hydraulic unit which the power steering pump supplies fluid to. You depress the brake pedal, and the hydraulic system amplifies your foot pressure. Your ABS, when active, "modulates" the pressure like Nikmike mentioned, giving you that pulsating feeling and noise when you are pressing on the pedal, press harder the pulses get stronger and louder, lighten up and the and they get weaker and quieter, take your foot off the pedal and it stops. It doesn't sound like your ABS has been active at all, test it out by finding a nice pothole at 35mph or higher, apply the brakes firmly just before hitting the pothole, when you hit that pothole your wheel will want to lock up, but the vehicle is still moving, the braking system sees this and will activate the ABS.
You didn't mention if the Wildwood package included calipers. 2 years ago I was towing a small travel trailer through the Blue ridge, and upper WV mountains, my perfect brakes revealed a nasty vibration after all that braking with the elevations. I either had or did have a stuck caliper that warped my rotor.
Is your warp showing up when the rotor is on a brake lathe just before turning it?

 

 

With that said, you should have the rotors thickness checked, and see if they are even still within manufacture operating limits. If he had to cut that much off just to get them true, you might have had a defective rotor, or it got extremely hot and warped very bad.

 

 

I think I'd be looking at those calipers. Check the floating pins, and check the piston(s). Wouldn't hurt to bleed again.

 

 

Not all code readers will read the ABS. You will have to locate a brand that will.

I worked in a brake shop long ago. We used to turn rotors all the time on most brake jobs. That is not the case anymore within the industry. Most brake rotor manufacturers are making the brake rotors so thin now, if you turn them once you are out of tolerances. I do not EVER turn the rotors on my cars/trucks nowadays. If there is a problem with a rotor, I buy new.

If you follow the break in procedures that sets the pads to the profile of the existing rotor, your brakes will work fine, provided the rotors don't have any deep grooves or surface irregularities that would prevent this. If I can catch a fingernail in a groove, the rotors get recycled.

Tom brought up a good point on driving style/braking style. Everyone is different, and all those different people get different life out of their brakes as a result. I see people all the time that have their front wheels COVERED in brake dust, while the rear wheels are shiny and clean. Those kinds of people are having problems others are not. I have a female family member (not my wife), who is pedal-to-the-metal from every stop and waits to the last second to apply the brakes before stops signs, turns or lights. Over the years, she has gone through brakes, shocks and other auto parts very fast.