BRAKES (Last update: 05/07/2009)
Figures that buying one thing would make me want to buy more...
The new wheels opened up the space between the spokes, so the stock brakes are highly visible... and highly ugly.

Despite the ugly, nasty, rusted, corroded look... the stock brakes are very good and enjoy a well deserved reputation for short stopping distance (116 ft @ 60 MPH), but they won't hold that over more than 2 or 3 rapid stops. So, autocrossing will place higher demands on the brakes than the stock components can handle.
"Big Brake" kit up front? New rotor and caliper for the rear?... Negative Ghostrider!
Once again, in order to stay in STS class for autocross, I have to retain the OEM spec calipers which essentially means I have to retain the OEM sized disks. So....
Power Slot "Ice" Rotors - OEM size, slotted, cadmium plated, cryogenically treated.
I had been offered a really good deal on OEM sized Brembo rotors from AWR, but they were unplated. Since I don't live in California, anymore, rust and corrosion resistance are much bigger factors in my planning and purchasing. So I went with Power Slot rotors for the cadmium plating. They also offer the rotors cryogenically treated by Frozen Rotors, hence the term "ice" rotors. Cryogenic treatment is supposed to increase the life of the rotors by improving the material structure of the metal to reduce rotor wear and warping. I bought mine on-line from The Tire Rack.

These rotors happen to be slotted. They look cool, but that's not why I bought them. There is an awful bit of debate on the effectiveness of slotting and cross-drilling of rotors. Based soley on all that I've read and heard, here's my opinion... take it or leave it.
1. Slotted rotors won't improve braking (much) if you use brake pads that don't "out-gas". Most of the newer performance brake pads are made of materials that will not significantly "out-gas" unless you bring them to near melting temperature.
2. Cross-drilled rotors will somewhat improve rotor cooling, BUT don't even think of getting them unless you are going to get an oversized rotor or so-called "big brake" kit. Cross-drilling on OEM sized rotors will simply increase the chance of the disk fracturing.
Goodridge Brake Lines - Stainless braided.

Purchased from AWR. These come with either stainless or zinc coated fittings. Being paranoid of corrosion, I went with stainless.
It took an overnight soaking of WD-40 and a 10mm flare wrench (or "line wrench") to break the compression nuts on the rigid brake lines without stripping the soft metal nuts. But with the wheels off and calipers unbolted, removing the stock rubber brake lines and installing the braided ones was not difficult or time consuming.
However, because of my custom AWR suspension, I did have to enlarge the holes in the metal support tabs on the struts to allow these cables to fit through and secure them to the strut with spring clips. Using cable zip-ties would have sufficed and saved me from drilling precariously close to the edge of the metal tabs, but they look much cleaner when clipped through the struts.
Hawk HPS High Performance Brake Pads

Also purchased from AWR. These are a great street performance brake pad, and they are very respectable for autocross. I went with HPS pads over the HP Plus pads mainly because the HPS pads are non-dusting. I know... that's a weak excuse... but I hate washing my rims.
Brake Calipers
Stock MX-6 brakes have earned a very high reputation for both their overall stopping distance and front-rear balance. With such noteworthy performance in the stock brakes, plus the requirement to use stock calipers for racing STS class, it looks like I will be sandblasting and painting them with a good high temperature caliper paint just to improve the looks, before I rebuild them.
I had originally planned to powder coat the stock calipers. I got a number of opinions on this, and finally decided to use caliper paint because it was less expensive up front, and easier to touch up than it would be to re-powder coat a chip. If you want to go this estra mile, A1 Cardone sells OEM replacements already powder coated, although the color selection is limited and I could not easily find a distributor that carried them.

Despite the good performance reputation, the mechanical reputation is troubled. The rear calipers on '93-'94 models have a design flaw that typically causes the e-brake pivot pin to seize the caliper (after 50K-100K miles, or so). This flaw was corrected for the '95 model. So, if you replace your rear calipers, check for this design feature. Compounding this flaw is a problem with the guide pins on the "non-bushing" side of the rear calipers corroding inside the sleeves. If the boots and grease on these guide pins are not well maintained, the guide pins will corrode from weather and contamination, also causing the caliper to eventually seize.
My rear brakes had both problems noted above. As a consequence of setting the e-brake too many times on a seized caliper, the threads on the adjusting screw for the e-brake tension were also mangled. So rather than refurbish the rear brakes, I am planning to replace the old calipers with new (not remanufactured) calipers. I will reuse the old rear brake mounting brackets. I attempted to puchase the calipers on-line from Summit Racing Equipment, only to find out that Dorman does not make them any more. Looking for another source, before I have to go pillage a bone yard.
The front brakes are in much better condition. As a pure precaution, I will also replace the guide pins and one of the caliper pistons that was nicked during disassembly with Dorman parts. These parts were purchased on-line from RockAuto. I purchased new boots and gaskets from the Mazda dealership. Otherwise I am reusing the remaining original parts while rebuilding the brakes.