Boot fitting is a process, but once they are dialed in, it's amazing! My feet never fit off the shelf. I wear a shoe size 8.5/9 and a 23.5 in boots. I have a short foot, wide ball, narrow heel, a very high instep and thunder calves (it's a definite family thing). I bought my newest boots last season and have been back to the boot fitter 4-5 times. The first 2-3 were pain issues, the rest are fine tuning stance issues (once the pain is gone, you can see other issues pop up). Now I can have them on all day without even loosening the buckles, but the first day I skied on them, I was in tears the pain was so bad and that was with custom foot beds.
You definitely have to ski on them, go back to the boot fitter, rinse & repeat. When the boot fitter wasn't were I normally skied (he was semi local to home), I would use a sharpie to mark exactly where my feet hurt (much easier to do when they still hurt). Take a picture or two so I could show the boot fitter, which could be days to a weeks later.