I think making a new pair of boots, or radically modifying the current ones, sounds like a great starting point. Provided the information for the fit comes from a highly competent fitter. By your descriptions, your experiences working through your current fitter have not been positive enough, IMHO, to presume that any aspect of his work should be taken as a good basis for making boots, or even for making the final adjustments post-manufacture.
I think that you should discuss with Riedell the possibility of traveling to their location in Minnesota to see their fitter, or if you can't afford that, to a fitter that they recommend, even if it is a several hour drive, before doing any further mods or getting new boots made. E.g., there is supposed to be a very good one who works the pro shop at the University of Delaware. Perhaps Riedell knows of one a little closer. Perhaps our New York members could also advise you on a really good fitter closer to home.
Yes, that sounds extreme, but you asked my opinion. My opinion isn't based on any knowledge of medical things, but is only based on working through the problems of misfit boots myself. It seems to me that the boot makers themselves, and perhaps the half a dozen to dozen best fitters in the world, are in a completely different skill category from the average pro shop pro. When your health is at stake, as it seems to be, it makes sense (to me) to go to the best. And the best for a given brand of boot probably are probably the people who make the boot, because each boot maker makes different assumptions on the way a boot changes under load. I'm not sure if Riedell will let you see the master boot maker, but they would almost certainly let you see a fitter that they have thoroughly trained to fit boots their way.
Too bad, with your location, that Klingbeil has been recently been criticized by people on this board for customer service issues. A couple of years ago, many people would have said that you try to get a refund from Riedell, and go to Klingbeil's factory store for custom boots. When they were run by the Klingbeil family, they were very knowledgeable and good - at least when Don Klingbeil (and Bill Klingbeil before him) did the fitting and mods.