Regarding the top of the foot pain, Barefoot Neil told me that it was a problem of doing too much too soon. I certainly can see that. I first got the pain after the harvest half marathon. While not the farthest distance I have gone in my Vibrams, I did more distance on gravel as well as went faster than I have ever done 13 miles before. A good 8 minutes faster. And then running up and down a mountain 2 days later probably didn't help. So I am going to take it easy for a little while till the pain goes away.
Speaking of pain, after our run yesterday I found myself with pain in my right heel all morning at church. It hurt constantly but worse when I walked. May have just stressed my foot a little too much yesterday or even worse could have given myself a stress fracture. Either way I am definitely going to take it easy and slow down. I would have thought I could do more since I have been running in my Vibrams for quite a while but these things do happen and I would be foolish not to take it easy until it is better. My wife however, who is still quite new to Vibrams and barefooting feels great (except for sore calves and her scraped toe of course). Annoying to me. ;) Not really, but so far she has transitioned well which is pretty good.