2001 saturn sc2 brakes

So did the pedal go to the floor before you changed the transmission?Do you have abs?Also if you have rear brake shoes and there out of adjustment that can cause a low pedal.

Is the tranny auto or manual?

yesterday bi found out the cylinder on back brake was leaking bad so i replaced it and im still having the problem also how tight should the drum be when u slide it on mine is pretty tight also it was a pain in the butt to take off on the side where i replaced the cylinder thanks

Does your car have abs?When you replaced the wheel cyclinder did you replace the two copper washers that go on each side of thr brake line with new ones?Also did you get the brake line tight enough?I have seen them leak fluid where the line connects to the wheel cyclinder.As far as the rear shoe adjustment you adjust the rear shoes up until when you spin the drums you can feel a light dragging from thr shoes rubbing thr drums.If the drums are warped or the drums have a lip worn in them it can make the rear shoes hard to adjust.