no i dont get it on the run at all which is wierd. its just like im getting the pedals pushed into my feet, which is why i started thinking i need new shoes

When I had an older cheaper pair of bike shoes, they weren't very stiff and I noticed my arches getting sore after longer riding, so I bought a stiff pair of generic orthotics (powersteps) in my bike shoes and it helped immensly.

Try some inserts from your running shoes in your bike shoes before you cough up too much money on custom insoles.

What kind of pedals are you using? Where are your cleats positioned? I doubt the soreness has anything to do with the shoe itself, but rather with your setup or insoles.

I second wilsondaj. What kind of pedals are you using? My tri bike has look pedals, my road bike still has the SPD pedals that came on it. I have stiff carbon shoes for both bikes. Last weekend I had an easy ride of 2 hours planned so I took the road bike out for the first time in months. My feet were killing me when I was done. They were numb right around where the small cleat for the SPD pedal is on the shoe. Took a while to feel normal again that day. Although I donn't ride much on the road bike I will be switching pedals real soon on that one.

I just looked in Andy Pruitts Medical guide for cyclists, and aside from echoing the advice already given about orthotics and a larger platform pedal, he suggests starting by moving your cleats back 2mm and lowering your saddle the same amount. This will redistribute the pressure on the foot, and possibly solve the problem. Also, you may be correct in your intuition about the problem being the shoes.... he goes on to say that some people need a shoe with a stiffer sole or bigger toe box (like RV and wilsondaj he recommends specialized).