Actually, you didn't have to worry about a little rag lint on the linings -- they'll be gone quickly. But you should keep everything clean -- using brake cleaner generously is a good idea.
Also, put silicone grease on:
1) the back of the pads, between it and the little metal plates (antisqueal);
2) on the short edges of the pads, so they can slide sideways in the caliper as they wear;
and 3) on the small pins that hold the pads in place, for the same reason.

Doing what you did about stepping on the pedal to clean the pistons' faces was not good -- you may find that you'll need a new M/C soon, even if it seems good now. If you ever want to extend the pistons, use your pressure bleeder.
All you really have to do for the piston's faces is gently clean it (and you can do that with them full retracted -- you don't have to be a perfectionist with this. But also be sure that the pistons' boots (the rubber ring around them) is clean and intact! And be sure that no piece of that rubber boot (e.g., a fragment) is "caught" between the piston and the back of the pads.