Lots of good suggestions here. For myself I tend to use the old school way of bleeding brakes. Make sure you have a drain line on the bleeder screws to a bottle or catch pan and keep a close eye on the fluid level in the master cylinder while going thru this process. Keep the cover on the master cylinder while bleeding. Pump up the brake lever 4 or 5 times but don't squeeze it to death, just a stout pull each time then hold the lever "in" maintaining pressure after the last pull. If the lever doesn't seem to "pump up" at first don't worry about it just continue on with the process. Open the bleed screw slowly and let the fluid and hopefully air bubbles flow out the bleeder. Close the bleeder screw before releasing the brake lever and repeat. This will no doubt take several cycles to clear the air out, watch your fluid level. If I am going to have a problem with a seal in the caliper because of piston overtravel I want to find out about right away, not later on. Keep an eye on the brake fluid level in the master as you are going thru this process as letting it get too low will once again introduce air into the system and you will have to start all over. This is a process that has been used for years and years and usually works for me. I always start with the caliper furthest from the master cylinder. If this doesn't work then you may have to try some of the other suggestions here or find someone with a power bleeder that knows what they are doing and can help you out. The only monkey in the wrench is if dirt/rust somehow got into the system and is plugging up an orifice. That usually requires complete disassembly of the master cylinder for cleaning.
Thanks for all the info, this is going to be my go-to thread for brakes work. The first bit of advice (from Rick) sorted out my problem but I appreciate all the other answers. When I opened up the bleed screw the next day more air came out, and I noticed that gaps between pistons and brake rotors disappeared. I guess the system needed time to re-adjust, I did push pistons in so I could remove the brakes and change the pads. I did put copper grease (prevents sticking) between pistons and pads and on brake guides before I installed the brakes back.
Thanks for all the help,