I changed my master cylinder because the brake pedal kept slowly going to the floor. I bled the brakes and now the pedal does not slowly sink to the floor BUT the pedal is low to the floor but holds the brakes.

I did not bleed the master cylinder could that be why? I pressed the pedal a bunch of time so thought any air in the master cylinder would come out? Would I ever have to adjust the brake pedal rod because of the new master cylinder?

 

Honda makes a tool for the MC pushrod length. It basically takes the length of the pushrod & transfers that to the booster, so you can properly adjust the pushrod length before installing the MC.

Most people check the length carefully between the new & old MC & hope they are exactly the same. That's how it worked out for me when I changed a MC.

Pedal being low to the floor (but not sinking slowly) indicates there's still air in the system. Probably the air is in the MC because you didn't bench-bleed it. I've had that happen too (before I knew about bench-bleeding) and got around it by continuing to bleed the brakes again. The fluid was coming out clear at the wheels & FINALLY some air came out & then all was OK. Buying more fluid was easier than R&R the MC again.

 

You need to bench bleed master cyl no getting around it.