I had very severe foot pain. It still comes back occasionally on the trainer, but not even close to as bad and it doesn't happen on the road anymore.

Here's what I had to do:

First, I got the Specialized shoes with the built in wedge. Then, I got the LeWedges and put two wedges on each shoe. That took care of almost all of it, and when I started keeping the shoe straps just a little looser the pain went away.

The point is, there are a lot of options out there, and you may have to combine a few things to find what works for you.