Sorry to hear you're having major problems.
I don't know what the solution is but the first thing I would do is go back to the guy that made the custom insoles, as they should be willing to tweak things until you get comfortable. What was the process the used to fit and make them?
Other than that, could the new insoles have reduced the volume of the boot so your feet are now cramped? If the bones of the forefoot are pinched together slightly it could cause that pain (I had something similar in cycling shoes with new insoles).