toes hurt too. Mostly the big joint of the big toe. Stretching them out some helps, sometimes I think the stretching does as much harm as anything. dunno
Asked the doc about it when I hurt my shoulder once. He asked what I was doing, and I described shikko, suwari waza etc.
He said "Of course your toes hurt! Don't do that any more!" Basically you're hyperextending the big toe when in keiza for example.
I don't ask that question anymore. ;-)
I think that glucosamine/condroitin (SP?) stuff helps some.