couple of things you can try:

start out with your shoes looser so your feet have room to swell. Make sure your socks allow for swelling also: no tight cuffs or elastic bands. Also you may want to consider switching out your insoles. I use running insoles in my shoes. I also flex and splay my toes while I'm riding so the feet aren't so static. I stop about every 1 1/2 hrs to eat and take off my shoes. I usually try to walk around in my stocking feet during that time especially if you can find some grass - it just seems to feel good on my feet!