Anytime that I ride anything over 5 or 10 miles, my left middle toe always hurts. Even after we are done riding it still hurts. It's only this toe and none of the others. I have clipless pedals, could that have something to do with it? Or is my toe just screwed up to begin with? Any ideas apprecaited.

Do your shoes fit ok or do they feel kinda narrow? If so can you loosen the straps or laces so your foot isn't squeezed?
Do you have another pair of shoes you can try?

How long after riding does it take for the toe to stop hurting?

Shoes feel okay. I wear them about as loose as one could wear them. It probably would hurt to get a wider shoe. The toe hurts off and on. Any day through the week if it gets extended when I walk, it will hurt then and from riding last night, it still doesn't feel "normal".

Any recommendations for brand/models of wider shoes?

like in this anekdote.

An ill-looking man comes to a doctor and says:
-Doctor, when I touch here (shoulder), it hurts, when I touch here(chest), it hurts, even when I touch here (legs), it hurts... What is all this???

Doctor looked,.... and said:

Your finger is broken!!

Your toe pain is triggered only when you get on your bike? If that's the case, your cycling shoe is the most likely culprit.