Way late to the discussion, but my arch pain in my last boots was caused by my boots being too long.
Let's see i I understand the basic idea. Because your boots were too long, the part of the insole where it bends upwards was too far forwards on your feet. As near as I can figure out, your foot is able to sustain an upwards bend near the ball of the foot (either because of inherent structure, or because we constantly wear shoes that have such a bend), but it can't easily sustain such a bend elsewhere. Having the bend in the wrong place caused some of your muscles, tendons, or other connective tissue to be continually subject to excessive stretching, or excessive compression.
If I'm right, it still comes down to the basic concept that if the shape of the boot doesn't match the shape of your foot, that gets you into trouble - not the excess length itself.
I'm using a pair of boots that are 1 to 1.5 sizes to large, without such problems. But I created foam insoles that filled space in such as way as to make them fit my feet perfectly, corrected for all balance issues, heat molded them, and I wear thick squishy socks. I love the result - though they are a bit heavy, which makes it harder to jump, and harder to control spins.
If your boots were both too long and too wide, there was space for you to have done the same thing. But hopefully you are happy with whatever you did instead. If a really good job is done on fitting and adjusting good custom boots, they can accomplish the same things - and weigh less.