Stronger Feet Make Faster Marathon Runners, Part 1: Skips for Height & Distance

Yesterday I did a 3 hour 20 min run in the hills at an easy pace 65-70% of max heart rate, well it was meant to be easy but my legs were still a little stiff and sore from my epic 2 hour midweek tempo run, so it seemed like a really long run!!!
I was wearing my modified Nike Free's, they feel great on shorter, faster runs BUT i could really feel the hammering to my feet and quads after the first hour, I made sure i was running with good form, but nothing really helped, I'm thinking I need a shoe that is light flexible but with good forefoot padding for my really long hill run, any recommendations?
Sun 8th
Run with Sarah on the sandhill 6, nice and easy, legs not too bad :]
Total time 1.11