Wonder if your feet swell up??, when u stop for 5 minutes the pain goes away? If your feet swell up that would contribute to the problem plus maybe a slight cleat move backwards could help also (5 mm or so)

I developed swelling big time in the last 3 years, started going from 43 to 44, then the problem was still there but took longer to show up, then went to 45, my dogs swell so much apparently that i dont even feel that the shoe is 2 sizes bigger, the problem (the same than u have) went away right away. I moved from carnacs to scott pro, then to specialized shoes with carbon sole (great shoes!!)

Good luck.