I drilled 1/2" mounting holes in my fender brace. I picked up a set of cobalt drill bits that made the task much easier. I wish I had bought a set years ago. They cut through steel like it was butter.
I used my bench grinder to take off just enough metal to get the brace to align with the lower shock bolts. When it was all done, the brace was only 1/2" above the tire. Nice and tight.
I have similarly tight tolerances on the right side where the brace clears the side of the tire and pulley.
Here's a side view without the fender...
... and one with the fender. I am planning to to cut the fender at, or possibly just below, the swingarm.
Here is where the mounting bungs will likely go.
Drilling the top of the brace and the fender itself will be next, along with making a bracket to bolt the front part of the fender to the swingarm. Then I will make a license plate bracket to hang off the left side of my fender brace. It's coming together...