Squishy Brakes

[RHarms]

My Cobra has been on the road for several years. The brakes have always been- adequate.
Recently the line entering the master cylinder, front, started to leak. Inspection revealed that the flare had broken. Long story short, master cylinder replaced and bench bled, line replaced, and a modified brake pedal was installed, to improve the pedal ratio. The brakes were bled.
The length of the rod between the power booster and master cylinder was not changed. ( I adjusted it incorrectly once, after driving about a 1/2 mile, the brakes locked. Very exciting)

Results:
1. Engine off, the pedal goes 9/10 of the way to the floor.
2. Engine on, the pedal goes all the way to the floor. Pumping brings it back, a very little.

For now, I assume the following,
1. Rebuilt master cylinder not leaking internally,
2. Bleeding done correctly,
3. Power booster OK.

Any ideas on what I should look at first? See above, I really do not want to mess with that power booster to master cylinder rod, but I suspect that needs to be lengthened.

By the way, the car was built and registered in New Jersey. I now reside in California. I am keeping my fingers crossed, re: registration.

Thanks