you have something going on with your running boards that I just noticed..
if you look at your before picture, the running board is tucked up against the rocker. this shouldnt be, there should be a 1-1.5" gap that is filled by a running board seal. in fact, if you compare how the running board attaches to the bottom of the rear fender but in the front has a 1-1.5 piece of the front fender hanging down, you can see what I mean. it looks like the whole bed/apron/running board got moved up to close that gap that usually has the running board seal in it.
what I cant figure out, is you have a stock cab on a stock frame with stock running boards mounts, and the gap is still gone.
so I am a little confused. in any event, if you lower the running boards that 1-1.5" for the seal, you will be closer to your 2" lowering goal right away.
gorgeous work too!