Running Barefoot... or Something Like It

Some years ago I bought into the hype created by the Nike Free running shoe. I was in the height of my short-lived running obsession and my knees were already starting to develop problems. I had run four or five marathons, a few half marathons, and a couple of 5 and 10Ks. I was getting fast, with a fastest marathon time of 3:27 and change. I had also been selected to join a study conducted by the Furman Institute of Running and Scientific Training (FIRST) with the promise that I could run fewer miles each week and still get faster. I wanted to run a 3:10 marathon and qualify for the Boston Marathon, so I had plenty of work left to do.
To make a long story short, I purchased a pair of Nike Free 5.0 shoes and began to train in them. My FIRST training plan helped me focus my workouts and limited the strain on my knees, and over the next 18 months or so, I PRed in every race I ran. I actually became locally competitive in all of my distances. I qualified for Boston with a 3:10:52 marathon and have never been anywhere near that since then.
Many things have happened between then and now, but it all boils down to a change in focus and priorities. It still nags in the back of my mind that I never actually ran in the Boston Marathon, and I want to do that. I also want to get faster. I would like to be a sub-three hour marathoner. I still intend to complete an Ironman Triathlon and even compete in Kona. That said, I have to beat back the 35 extra pounds that have managed to acquire while in Alabama, make time to train, convince myself that it's worth all the pain and suffering, and so on and son forth.
I have had a few false starts over the past year; results of aggravating old injuries, lack of time, and general laziness and apathy brought on by 35 pounds of fatness. I have found that my favorite Nike Free shoes no longer work for me, and although I have a pair of Saucony runners that are quite comfortable, they make running unpleasant at best, if not downright painful.
So this week I splurged and bought another pair of barefoot-style running shoes, the Vibram Five Fingers. I bought the KSO model for $85 and have begun running in them.

 These are as close to barefoot running as I dare get (at least on the road,) and I have come to determine that even the Nike Free is nowhere near the level of barefoot running commitment that these shoes are. These are little more than a fitted rubber sole attached to some aqua-socks mesh. There is ZERO support, cushion, or anything built into these things. (Kind of makes you wonder what the $85 pays for...)
Like the Free, these shoes come with the instructions to wear them for a couple of hours a day for a week or two just to get your feet and legs used to going barefoot, and then gradually work into running in them. Yesterday I ran a slow mile in them and I had to completely alter my gait. I can't imagine heel striking in these shoes. For a brief time before buying my first pair of Frees, I ran barefoot on a large grass lawn and found that I had to run on the balls of my feet just to keep from jarring my legs with every step. The Nike Free has a thick cushion on the heel, so I was able to resume heel striking, but the Five Fingers do not, so I am going to have to commit to changing my gait entirely or give it up.
After a mile yesterday and two miles today, my calves are faring the worst...Imagine tiptoeing for two miles and you've got the right idea. I can stretch it out pretty easily, but I will have to be very careful with how I begin training again.