Well that doesn't answer my question! :P
I believe that training in bare feet, starting small, progressing slowly, can probably yield positive benefits. The reason I didn't consider it before the injury? I could hike 20+ miles a day, never had sore feet, ankles, calves, etc. No blisters, no bruises, no nothing. Why fix what isn't broken?
Injury happens. Try different things: changing shoes, footbed, running surface, frequency of workouts, etc. No bueno. Going barefoot is painless. Sweet. Rock the bare feets a while. I'll keep doing it too, as long as it doesn't hurt. But..
If I am to approach the problem from the perspective of regaining what I have lost, or as we say in nursing, returning to prior level of function, can the barefoot philosophy return me to hiking as I previously did? With the goal of "thru"-hiking the PCT in 2014, I can hardly expect to show up in Campo next April in a pair of huaraches and hike 2600 miles in 5 months. The goal seemed totally obtainable (in my brooks cascadias) 3 months ago, and seem highly unlikely in a pair of comfortable, if inappropriate, Lunas.
So, I'm keeping up the biking, stretching, etc, with the intention of returning to modern footwear, even if it costs the respect of more enlightened individuals. I'm doing to keep rocking my flops, or bare feet, too. Because it is comfortable, and because I think it is beneficial, bit by bit, to maintaining strong feet. Who knows. Maybe years from now I will walk the PCT in huaraches, but probably not in 2014.
Disclaimer- I just demolished a sixer of Fremont IPA, and I'm not entirely sure if what I've just written makes sense to the sober.