OK, so there are a lot of what if's to my reply and I am basing my response on my experience with a 33 ford.
1) did you use an aftermarket kit or a real mustang II unit. If it is a kit, call the manufacturer and ask them how to remedy the problem, the probably planned for it.
I installed an actual Mustang unit in my truck and ran into two problems. One, the upper A arms hit the fender. Two solution: cut a hole in the fender and build a recess for them or change to a tubular a-arm setup (I cut the holes b/c at the time I was in high school and didn't have the funds).
As for the fender braces themselves, you probably won't like this answer, but I moved them. I acually changed from the 32-34 truck braces to car brace and relocated it slightly. It may not be the pretties fix, but it works.
I stress again that these were problems on a 33, but I imagane the problem isn't too different. Good luck