Without a pic it's hard to tell what you're looking at.
The stock brake linkage is adjustable. The shaft from the master cylinder goes down through a clevis that attaches to the back of the brake pedal arm. The stock setup has nuts above and below the clevis. The top nut could be hidden by the rubber boot in the master cylinder and the bottom nut is "inside" the clevis.
When I welded up lower foot peg mounts I needed to remove the master cylinder so I could clearly see all the parts andget the nuts as high on the shaft as possible. This put the brake pedal as low in front of the footpeg as possible.
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