I make 46mm Webers from 40's so I understand the topic. Stock 46mm butterflies are available from PMO however there is an angle associated with them, they are ellipses; both Webers and PMOs use 78 degree ellipses. I suspect this isn't an issue with MFI but for carbs it is critical for the ellipse angle to be correct to make progression holes align with closed butterfly. The depth of the bore through your stacks appears to be quite long for my tooling but I think a good machine shop could help you both with the boring and the slot lengthening for the 46mm butterflies.
A step from smaller to larger is OK, a stem from larger to smaller is not good at all.
Paul Abbott
Performance Oriented