I worked on hundreds of these, the brakes stopping short is more than likely excess brake dust in the drums. You can jack it up and pull the wheels, use a can of brake clean with the spayer straw on it and spray the cleaner through the ajuster hole in the backing plate and turn the drum by hand and let the cleaner run out into a pan.

The clunking noise is either mast trunnion bushings worn out or the drive axle trunnion caps need to be removed and ground down about 1/8 of an inch and they can be removed without pulling the mast off if you are patient. You probably know how to check the mast trunnion bushings, but the drive axle caps can be checked with a big pry bar while the front end is up and wheels removed just wedge the bar between the axle housing and frame and see if it shifts. You're also probably going to want to change the motor mount bushings too when you do the axle trunnion caps because they will wear prematurely if the front of the drive line is moving around. If it's clunking it's more than likely the axle tunnion caps when you hit the brakes the entire drive line is shifting forward and back.