I have an arrangement with my boss to have a "standing" work area (have you read the article, "Sitting is Killing You!"?) I can also wear my VFFs everyday to work. I work at in an IT call center so I stand at my computer anywhere from 8 - 12 hours a day, 5 days a week. The first week I started this I had been wearing my VFFs for about 3 months, and I though I had my feet broken-in pretty well. However, after the first couple days my lower legs were sore, my feet were very tender and my lower back hurt. I persevered. I started reminding myself to shift my stance regularly by using Pilates and Ballet stances and I also stretched my toes and arches by bending my knee forward (like a walking step). After only about 2 weeks I didn't even notice if I had been standing all day. My feet stopped hurting all together (along with all the other aches and pains) and I actually had more energy. On a side note, as I was getting use to standing so much, I did find my KSOs were more comfortable in the beginning than my classics or Bikilas. Now I can I even wear Performas and I am good to go!
So, after taking the long way around the block, I would recommend you shift your stance regularly and try to stretch your toes and feet from time-to-time (just like you would stretch your fingers and wrists). As with everything, go slow but do it consistently to give your body a chance to adjust to it.
Hope this helps!