I may be wrong but doesn't a 2006 SB have the mid glide front end with 49mm tubes? There's likely nothing wrong with your brakes other than they just aren't very powerful. The change was documented a while back in Hot bike, installing Fat Bob sliders (you need both - fender mount is also different) a second disc and caliper from the FB and modify your fender mount holes to suit the sliders. You'll need a set of stock FB brake lines and an 11/16" master cylinder. If you get the parts online and save 20% its not too bad, for the MC on mine I used a take off touring MC which fits and works fine and looks better too. The second disc gives you the 2 finger braking that should have come from the factory like a Fat Bob does and NO - its not at all over braked and is very controllable. I had a mountain lion run out in front of me over the summer, hit the brakes in time and only clipped its tail.