If you readjust the pedal stop so that the pedal is resting at a higher position, the brake rod that runs back to the rear brake will require adjustment.
If you don't adjust it, it the pedal will go clear down to its present braking position before it does anything.
After you loosen the stop bolt and adjust it so the pedal is at the height you want it to be, re-tighten the jam nut.
Then go to the rear of the bike and notice where the rod passes thru the brake arm that is on the rear brake.
There is a nut on the rod that will need adjusting. This nut usually has a hollowed out area on its forward face that mates with the rear brake arm.
I like to put the bike on the center stand so the rear wheel is in the air.
Once done, tightening the adjusting nut while turning the rear wheel will begin to apply the brake even though no one is pressing the brake pedal.
If this happens, unscrew the nut a turn or two so the rear wheel can turn freely. Then try the pedal to see if it moves to your liking. If not, play with the adjustment nut a bit more.