Too bad you didn't mention this before changing the brakes. In your "before" photos the cable anchor for the front brake is installed at the top of the headtube and above the headset's upper race. Given your large frame and the long steerer span inside the headtube that is a common source of pulsing and vibration under braking with canti brakes. Lennard Zinn (who is also 6' 4" or more and a frame builder) has written rather extensively about this phenomenon.

The cure is to mount the cable anchor at or under the bottom of the headtube and there are adapters that use the caliper brake hole in the fork crown to accomplish this.