+1, the closer to vertical that the arms are when you're applying pressure, the better too.
Also had the same issue with my mod. I removed the zip-tie from the cable boss closest to the back tire along the top tube and sliding the cable a little this way or that way cleared the problem up. Had something to do with the angle of the noodle and how it approached the brake arm. Putting a small gentle bend in the cable just as it exits the noodle can gain you a few mm too, but don't kink it so much that you unravel the cable wires. Hope you get it sorted, and hope my explanation might help.