Don't worry. Mine doesn't hit the rubber bumpstop either. I did the conversion on my '70 2 weeks ago. I got the bracket off of a '70 that had the power brake option. I just used it as a good excuse to have my brake pedal closer to being even with my gas pedal, so that it is easier to get my foot on the brake pedal. I hated how high it was before power brakes. My pedal doesn't move much at all, so I'm not worried about hitting the floor.
I don't think your doing anything wrong. The only thing that I can think of, is to replace the pedal assembly from a pwr brake truck. I took the pedal assembly from the donor truck, but didn't care enough to swap, or even measure to see if there was a difference. I just don't worry about it.
