If you need to replace your...
If you need to replace your pistons, you may want to consider an upgrade. All Wilwood calipers now come standard with these heavy wall pistons (left), which exhibit less flex under load than standard stamped pistons (right). This can contribute to a firmer pedal and more feel for the driver.
Once the calipers are clean, take a moment to check the caliper bores. They should be smooth, especially on the thrust side (the side of the bore opposite the direction the rotor is turning) Bush says that some anodizing wear is OK. Any small scratches or buildup from boiled fluid can be buffed out with a Scotch Brite pad.
Bush also says that you shouldn't have to remove the caliper's crossover tube, especially since it can be difficult to fit a wrench in that area to remove it. If you decide to remove it, make sure there's a new bead of silicone for the tube to sit in once it's reinstalled. The silicone not only helps hold the tube in place, it also damps vibrations that can eventually cause the tube to crack.
Rebuild kits are available from your manufacturer and usually include new seals and metal clips for the pads. Bush recommends always replacing the piston seals on every rebuild, no matter how good the old seals look. Repeated heat cycles cause the rubber seals to harden and become brittle. This not only makes the seals more prone to cracking, it also reduces their ability to pull the pistons back and away from the rotor and can lead to brake drag.
Once everything is clean, trial-fit the pistons into the caliper bores without the seals in place. They should slide in and out smoothly and spin without catching. If they don't, you may have to spend some more time with the Scotch Brite pad. If the piston movement is smooth, place the seals inside the groove in the caliper bores. Leave the seals dry for installation; they should go in place with only finger pressure.
If you are having trouble...
If you are having trouble boiling your fluid, one possible solution is Wilwood's new Thermlock(r) piston. Bush says it is being used by NASCAR Nextel Cup and Craftsman Truck teams at Martinsville. It does such a good job of insulating the brake fluid from the radiant heat created at the pads that teams running them have been able to do away with brake recirculators.
Next, insert the pistons back into the caliper bores. The fit is tight, so it may require a little work to align them properly. You should never have to force them or use anything other than your fingers. Also, make sure that the pistons are bottomed out inside the bores (the top of the pistons will be nearly flush with the inside face of the caliper). If you are installing new pads, the pistons have to be completely retracted so that the pads fit over the rotor. Then, insert your piston stop again and test the pistons using the air chuck. They should extend at approximately the same time. It's better to discover a stuck piston now than on the racetrack.
Finally, reinstall the bleed screws. Bush says that Wilwood bleed screws are tapered and self-sealing at the proper torque. If you use pipe-thread style bleeders, however, you will likely need to use thread sealer. If this is the case, be cautious so that you avoid getting sealer inside the caliper body. Thread sealer can contaminate the fluid. Bleed screws should be torqued in place according to the manufacturer's specs. While you're at it, recheck the torque on the bridge bolts as well.
The last step before reinstalling the calipers on your race car is to insert a fresh set of brake pads. Now that you've come this far, don't just slap in the pads and assume that everything is OK. Make sure the pads slide back and forth inside the caliper without sticking or catching. If one does, use a file or grinder to bevel the edges of the backing plate. Reinstall the calipers and begin flushing the fluid throughout the system. If you've also changed the rotors, don't forget that you may need to take a little extra time at the racetrack to bed in the brakes. And with that, you are ready to go racing!

Remove the piston seals with...

Remove the piston seals with a small bladed screwdriver, but be careful not to scratch the caliper bore. Inspect the bore by feeling the inside with your finger. It should be smooth and free of scratches or rough spots.

After the piston and caliper...

After the piston and caliper bore have been cleaned, trial-fit the piston back into the caliper bore without the seal in place. It should slide in and out and spin freely using nothing more than finger pressure.

Fit new piston seals back...

Fit new piston seals back into the grooves in the caliper bores. New seals are inexpensive, and the risk of re-using the old ones is too great.

Before final installation,...

Before final installation, lubricate the piston wall with a little brake fluid. This will help create a good seal and stop any leakage the first time the brakes are applied in the race car.

You should be able to reinstall...

You should be able to reinstall the pistons using nothing more than finger pressure. The fit is tight, so the pistons have to be absolutely straight to go in.

Reinstall the bleed screws...

Reinstall the bleed screws and torque the bleed screws and the bridge bolts back to manufacturer's specs.