Been getting terrible pain in the feet of late. about an hour into the ride they start aching and then if i stand up it gets a lot worse, so much so that on the downhill i can only stand for a very short time before the pain becomes too much.
I have flat feet so figured that might be something to do with it, so moved the cleats back on my shoes as i thought it might be that they we too far forward and bearing my considerable weight too near the end of the shoe, but that hasn't helped.
currently I'm using shimano xt pedals and shimano am50 shoes. Will bigger pedals help by supporting the foot, or even flat pedals?

My feet used to ache if I tied the straps too tight. Restricts the blood flow or some such. Might not be your problem though.

I have weak arches and did suffer from plantar fasiitis. I ended up seeing a chap called Mike Veal at Bikedynamic and having my pedal stroke analysed. I now run a combination of in the shoes wedes and cleat wedges to compensate for my varus tilt. Much better now.

I used to get this, though not as bad.
Stiffer soled shoes, looser straps over the front of the foot and a pedal with a bit of a platform (CB Candies) workd for me.

are the specialized body geometry shoes any good?

are the specialized body geometry shoes any good?

Yes they are. It would be beneficial if you could get to one of their concept stores to get a proper shoe fitting.

I had a similiar experience to you over the weekend, feet were in bits after only a few hours of a big event. I loosened straps, changed socks, tried to pedal differently but nothing worked. I have come to the conclusion my Sidi shoes just don't have enough cushioning for me for longer events. Out last night in my old spesh shoes with no issues. I too have flat feet.

Apparently it's all to do with the metatarasal area.

Have a look here.