I have a 93 Prelude and I changed the master and slave cylinders. I bled the whole system with a vaccum bleeder so im sure there is no air in the lines but the pedal is not as firm as it used to be and there are no leaks.

What do I need to check?

I know on the master cylinder is a nut to adjust the length of the little clip that connects to the pedal. Could adjusting this clip make it better?

Thanks

 

Try manually bleeding the clutch system first and yes you can adjust the push rod to change the free play on the pedal.