Look at the pic right above your post, it's my bike with lowered pegs (down 1" and back 1"). Notice the threaded portion on the master cylinder rod, it's shorter than the stock setup IIRC. What I had to do was disassemble the linkage enough to grind the lower end off of that rod: 1/4" - 5/16". This will allow the rear end of the brake pedal (at the clevis pin), to draw upward enough to lower the pedal itself. You can also see how far the brake is below the clutch cover and where it was scratching.
Without grinding the end of the rod off, it hits the
rear end of the brake, preventing the pedal
from adjusting lower (higher at the rear). Removing 1/4" - 5/16" will still allow the brake pedal to be set back up to the stock height.
I also had to extend the brake spring about an inch, it was too tight. You can see the gaps between the coils.
Well, I understand what I said.