the primary adjustment to the brakes is on the brake band under the seat. You can adjust them from the back under the seat if you want. It's nice to have a short wrench or some channel lock pliers etc to work under there. Harder to do it with rear mounted equipment in the way, but if you have good eyeballs on the ends of your fingers, you can do it! Adjust the steering clutches while you're there.
You may have gotten more room to push the pedal, but you did not adjust the brake properly by changing the length of the linkage rods under the floor boards. You probably should put them back before you adjust the brakes as the pedals may bottom against the upper stops and lock the brakes before you get the brake band mechanism back in the correct position. As you apply the brakes, the brake operating lever needs proper travel between braking and released positions so the brakes release completely.
Notice the procedure to adjust the brake band support screw underneath the tractor.
The pulsing of the pedal is because the brake drums are not perfectly round and since the bevel gear shaft rotates much faster than the sprocket shaft, you feel the rapid pulsing. These can be dressed on a lathe if you have the steering clutches out for repair.
Pulsing brakes can also be the brake drum can be loose on the final drive pinion. If you can pry the drum up and down it will tell you if it's loose. Hope they aren't. Charlie