In reply to Nath93:
I have the same problem with Nepal Extremes, though not all the time - some days are fine, some terrible. I have very high arches, a bony instep and narrow heels and have trouble with lots of boots of various brands. Scarpa are too wide and in my size - 47 - too short for their width.
I had a custom orthotic footbed made and this helped a lot. You stand on a scanner, they 'scan' your feet and see where the pressure points really are, then make each footbed accordingly. My left and right bed are quite different, as my feet are quite different. Under the ball of my right foot is an extremem pressure point, owing to the shape and dynamic of my foot, so they put different padding there. They also put a bulge of padding under the middle of my foot, where there was an invisible space, to take some of the weight.
Superfeet and other regular shop footbeds can only do so much. Likewise different lacing, shims, wedges, pads and various things never really helped. Very few shops can fit boots well and all have limited resources, particularly compared to a professional maker of orthotics.
They're very expensive, but I feel they're worth it in the long run. Mine are almost finished now, but have lasted around seven years of intermittent but heavy use.