I guess I'm a little late on this thread too. It sounds like you have solved some of your trouble. I had BellTech shackles on mine before I dropped it down more to a 2/4.
I used a DJM 2/4 kit that had a 2" front spring, with shackles and hanger for the rear. After I installed the hanger kit, I had to put the DJM shackles on. The BellTech shackle would not allow me to raise it up a notch to prevent it from bottoming out. The DJM shackle did the trick.
Mine will bottom out still, but it takes quit a bit to do it. I think the stock rear spring is too soft. 2002harley probably has the best solution using the F-250 overload spring. I may try dropping mine down again, and add an extra leaf, without a C-notch.
Good luck with it...