I just re-installed mine. I have Steeda Ultra Light springs which drop the rear about 1 1/2" and the front about 1" and I don't have any clearance issues. What springs do you have?
I'm sure you have it right, but make sure it's installed correctly, i.e., it tappers from the front to the back. It may be rubbing on the e-brake bracket...some folks have had to relocate it. Lastly, you said you checked your pinion angle, but may want to triple check that.