All of what you described is fairly normal. Your toes will definitely adjust over time and spread to fill the toe pockets. The toe rubber does go over the top of the toe. I have a slight Morton's Toe(2nd toe longer then big toe) so my length is based on fitting that toe vs the big toe.
I think you might be trying on "too much" shoe. Start with some KSO's. Get used to the whole VFF feel at a much lower price. To me, the Bikila sole(Speed) is a bit more specialized, as it almost forces the outer toes to be higher off the ground at rest(I think to keep them out of the way when running) and thus you need to have more experience with VFF's in general to pick out whether the Bikila/Speed fits right. Try on some KSO's at REI, get your size, and then order from one of the super deals that are available on the web right now.
VFF is an acquired taste. It took me quite a while to go from my first pair of KSO's to my next pair of KSO Treks. Then within 3 months I'm up to 6 pairs.
Start slow, grasshopper
