Man, I feel your pain. I'm fighting the same thing. Here's one of the best diags I've found which happens to be my parts too:
http://www.classicperform.com/TechBo...htm#rightvalve
My mechanic says the travel (assuming the booster is ok) might be a brake not moving properly due to blockage, leak, stuck...yada. He suggested clamping the flex hose(s) to isolate which wheel. My rear only has one flex hose at the tee. And with posi trac, I can't rotate just one wheel. When I clamped that hose, I had little pedal travel. So, I'm thinking one of my cylinders is sticking. I noticed a difference in travel with shoe adjustment, but I don't think that's all. I might go ahead and replace them since they don't look as new as the rest and I can clean the lines out more.
I hope this helps. Good luck and keep us posted