Before retracting your calipers (ie. before you remove the calipers), you should have bleed off some brake fluid. This keeps little particles from seizing your calipers later. If you didn't do this friends and I have found you have a 50/50 chance of them seizing (where we live anyway). [It sounds like you already took the calipers off, so before retracting them open the bleeder so the fluid will evacuate as the piston compresses.]
You don't need any special brake bleeding kits. Use a bottle connected to soft hose. Have somebody in the driver's seat press the brakes while you open and close the bleeder valve. Keep going until you either have no air bubbles in the system (you shouldn't have any since you are only replacing the pads) or until you see fresh fluid coming out.
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Watch the level of brake fluid in your MC and keep topping it up with DOT 3.
I personally like to replace rotors each time I replace pads. That's pretty straight forward, just put on the new one the way the old one came off. Wash them before installing with a soap like simple green or dawn.
While you still have the old brake pads you can retract the caliper piston by placing an old pad against the piston and using a clamp to push it back in.
Load up new pads into the caliper and slide it back over the rotor. If you have a new rotor it may take some force to get it to slide over. After you get it on you will need to line up the caliper mounting bolts — be careful that you get them aligned before starting the bolts so that you don't crossthread them.