In a good working system with an adjustable pushrod, a person can set the amount of pedal travel, before brake activation occurs, with pushrod length. As long as your pedal gets hard before it hits the floor, your pushrod is not too short. It may not be ideal, but it's not too short.
If the pedal rises with multiple rapid pumps, the rear brakes need adjusting.
If the pedal never gets hard you most likely have a hydraulic issue. It could be mechanical, but more likely it's hydraulic. The clamped rear wheel cylinders will point to the right direction.
The pedal needs to park at the factory location. There is a stopper at the top that it is supposed to bang into. The spring in the M/C is the guy that does that, in conjunction with the pushrod length. Do not use the brake-switch as a stopper.
As to the honking
Hmmmmmm, I'm gonna go with a mechanical sound of rubbing parts, but that's just a guess. Perhaps the pushrod on the firewall. I can't see that, but....... IDK
