Although my knowledge of Iaido is limited (one book I have read on the subject) I feel that you would greatly benefit from Hindu squats.
Go to http://www.stadion.com/column_stretch22.html
and it will describe better than I can how to do this exercise.
It will not only build flexibility into your toes but in your knees and legs as well as strenthening them (no more aches and pains after sessions!)
Try them and let me know how you get on.