Brake Pedal Diagnostics

Just a thought.

If with the engine off, you can press on the pedal and it is firm and does not go down to the floor, AND you can hold it without the pedal sinking over time.

Then perhaps the linkages are not matched correctly

When the engine is running the booster will pull the pedal down more than your leg alone can move it, but only a 1/2" to 1"

So if the linkages were not matched correctly maybe you are already close to the floor and 1 inch bottoms it out.