in general, high rotating mass machines like bush hogs, silage blowers, and anything without an over running clutch are not to be stopped from full speed by disengaging a braked PTO. The brake is typically designed to hold a shaft still that is already stopped that has a few ounces of drag on a pilot bearing. Any load greater than that will ruin the brake component. *emergencies who cares about the machine* (although the brake may not stop it any faster than the below method)
Normally you should keep the PTO engaged, and throttle the tractor down to idle (sometimes in steps), let the RPMs stabilize and when the implement speed is as slow as possible, disengage to a coast/neutral position if available, then brake position.
You probably did some damage braking the PTO shaft from full speed, But usually it takes more than once to ruin a PTO brake.
I'm not familiar enough with the technicals of that tractor but you probably have 2 issues that are related but not the same issue as the PTO drive and PD are in the same housing.
Hope you get the more technical answers you seek.