I agree. I haven't run nearly as much as you, but I did run shod about 15 miles a week for almost three years 10 years ago, no problem. Since running barefoot again, I've gotten typical running injuries I never experienced before, like ITBS, but I would nevertheless never go back to shod running.I think it's hard for me to put into words how better off I feel running barefoot.
P.S., I still think you guys should consider the sore tendon-tight muscle connection