So your saying the black piece in the second photo is the piston? But if the bore of the cylinder is 1 1/8 that black piece should be close, within thousands, to the same size as the bore. It's barely 5/8", doesn't make sense. In the first photo the black ring is a snap ring that holds the piston in the bore, if you remove that you'll be able to get the piston out, but you probably don't need to.
As far as pedal ratio. Say the distance from pedal pivot to push rod attachment is 3", and from pedal pivot to foot pad is 12", that would be 4:1. But you can't just re-drill the pedal arm to move the push rod attachment as that will change the arc of travel of the push rod and may put it in a bind, or push it over center. The best thing would be to lengthen the pedal arm to 18", but I can imagine the headaches that will cause, or change the pivot attachment of the pedal arm, even more trouble!
Reading back over your OP, maybe time to check that everything you swapped out is the correct stuff.