Drum brakes and disc brakes have vastly different pressure requirements. The extra valves in the drum brake cars are there to reduce the pressure to match what the drums need to actuate properly. A drum brake is to some extent self-energizing, which means it doesn't require nearly as much pressure as a disc brake. If you were to remove the valves on the drum brakes, you would be locking the rear tires a lot and very badly. If you switch to Disc brakes, and have all of the right hardware to go with them (do you have the right ABS module, etc.) only then can you drop those extra pressure limiting valves.
In regards to the discussions that Josh and I have had offline, there really isn't a whole lot beyond what has been posted already. But I'll see if I can summarize.
First, deleting the ABS is rarely a good idea. Even on a race car, ABS will prevent you from flat spotting expensive race slicks . . . Plus, without ABS, you have to be 100% attentive to your braking 100% of the time, and even the best drivers brain fade sometimes, and while some of us here may be halfway decent on a track, I'm pretty sure none of us can be ranked among the best in the world (unless Schumi started posting here and I didn't know. . . ). ABS is a safety net, and probably should be left in place, especially if you aren't trying to race the car competitively (where that extra 10th of a second may make a difference). Also, the electronic proportioning used in the later cars at least (called EBC) has a better control of the rear brake bias than any aftermarket bias valve you can buy, even the big $$ racing parts. The EBC can dynamically control the rear pressure at all stages of a braking event and vary them as necessary to give you the maximum braking without locking up. Given the very large front weight bias of the contour (and most FWD cars) the rear brakes do very very little in relation to the front, so you want to use the rears as much as possible to take some of the thermal load off the front brakes and keep the car balanced, but at the same time, during a stop the load transfers forward even more, which leaves less and less traction for the rear tires for the brakes to use. Switching to a basic aftermarket adjustable prop valve will leave a TON of brake usage on the table if you set it to where the car is actually safe to drive. Not to mention the need to use one valve in each rear line and to keep them synchronized somehow.
Now, I don't mean to imply that the Contour ABS/EBC is the greatest in the world, just that to get to something better would require a budget of significantly more than anyone on this board would be willing to pay, and would require a car on the level of one of the ProDrive BTCC mondeos for it to actually make a difference.
Aside from that, Josh and I talked about some of his caliper and rotor choices, and basically I just cautioned him about keeping the same hydrualic ratios between the master cylinder and calipers as the stock parts have, otherwise the pedal feel and line pressures will be garbage. Also, going any larger than the warmonger rear rotor kit won't be much of a benefit, because the EBC will end up taking away more line pressure in hard braking situations. Oh, and that brake pad area has very little to do with the amount of brake force generated, but does play a factor in pad life and some other secondary concerns.