Brake pedal clearance

The brake pedal movement goes down to about 75% from the usual 25%. Im wondering what could have caused the sudden change of clearance. No sign of leaks, tires are still screaming when I hit the brake hard but I think my stopping distance has increased. It seems like only the front brakes are working hard. Could it be possible that one of the rubber caps in the master cylinder has worn-out? But why so sudden? I changed the rubber caps 4 years ago. All oem. Hand brake position and hand braking power is the same as before. All brake pads and shoes are still thick.

This started a week ago right after we changed the gearbox. We did not touch the brakes or any line. I just remembered using the brakes so that my friend could loosen the nut on the axle. Help!