Did he measure the ball of your foot? Your feet should not hurt. I would also be concerned that eventually it will put stress on your knees. Foot placement is crucial or it can lead to more serious problems.
He's wrong and some readjusting needs to be done. I would recommend gloves for the cushion problem. I've gotten twitches in that area especially after Mt.biking. You need something to pad those sensitive neves. Maybe you need to loosen your grip a bit. Are you overextending to much. It's amazing what a cm will make it the stem.

BTW how did he fit you? Did you take all your measurements and put them in a computer? I've found that's the most accurate way.

Kim