What you are experiencing is not uncommon after the type of repairs you had done.
What has occurred, is over time the master cylinder bore has corroded from the water the brake fluid as obsorbed.
With new pads installed the piston in the master cylinder is resting at a different location in the bore than before.
The seal is setting on the rust, and as such it has it's pressure bled off.
This is your failed pedal sensation.
The cure is rebuilding the master cylinder, provided the bore can be honed clean.
If not the bore can be sleeved, using bronze or stainless steel.
Rebuilt master cylinders are available, exchanging your's for thier's.
Check it out.
Happy Trails Beep Beep from Houston!!!
Donald, El Cheapo