I've had similar problems.
I then bought some new shoes, the problem dissipated somewhat.
I have now got a third pair of shoes and have come to the following conclusions:
The cleats need to be towards the back, so under the back of the ball of the foot rather than the middle or front of the ball of the foot.
Socks need to be slightly thick (not walking socks, but defiantly something with a bit of pile)
The shoes need to be trainer touring type shoes, not the carbon roadie clip in things with the rachets
Depending on the shoe I'm normally a 9 or 9.5, I deliberately got them as a size 10
Don't do up the laces too tight, especially at the front.
With my roadie tight shoes I can do about 20 miles before agony creeps in.
In my touring trainer type shoes I can do 127 miles in a day and be almost pain free on the feet (other bits may be in agony, but that is not the fault of the bike!)
So my roadie shoes have now become my commuter shoes and my Touring trainer style shoes are for anything over 10 miles