It was most times applying the brake.
Edit: for clarity, the pulsing went away with the master cylinder replacement. So what I thought might be warped rotors was resolved with this fix.
I just did this. Opted for the full unit for $1300 because I worried that I would do the motor and then the accumulator would fail or something else. It also saved a decent amount of time not having to move parts over to my old unit.
One thing I wanted to share was my braking started to feel...