OK - first of all, I haven't been posting for a while. I intend to do a certain post then don't then put off other posts until I do the first post. Forget it!
A while back, I did a hard workout one day and then a recovery run the next. Some funny thing was going on with one leg which got more and more sore as the run progressed. At just about the midpoint of the run, I had to stop running. So I tried going barefoot and the pain went away immediately. I had another workout prior to this where I ran a 12 or 14 hour tempo run at 7:30 pace. When I got off the track, something started hurting right away. So I ran home barefoot on that occasion too.
There are several adaptations necessary for those going from shod to unshod running. The first thing is that your heel is going to drop farther and you'll give more work to your Achilles tendon. I think you should not try to run on the balls of your feet (i.e. your heels should come down and you should have a relatively relaxed calf when your foot is resting on the ground. The way to gradually get into this is by wearing flats or by running in grass. Another potential adaptation is to run with a more erect posture so your ankle doesn't need to flex as much.
Impact to your foot without that cushioned sole is also something to be managed. You can't land heel first on a hard surface and not hurt yourself. Landing heel first also seems to me to be a good way to sprain your ankle. So basically, I think you want your lower leg relaxed when it is off the ground, then land on the ball of your foot. This turns out to be close to flat-footed for me when I'm running on pavement. The other adaptation (which works well without the weight of the shoe) is to have faster turnover. This lessens the time that gravity has to accelerate your body toward the earth, thus lessening the impact when your foot does hit.
Finally - blisters. I can run 4 to 8 miles on concrete sidewalks without getting blisters but I will get a hot spot. Wearing moccasins is one good way I've found to avoid this.