[asid61]

+1 on using a smaller custom rod.
Using a 3/8" hex shaft could be possible if you used custom Dog stuff, but ballshifting would be very tricky. On the plus side, you could use the 3/8" x 7/8" flanged bearings, which are very compact, for your dog gears.
Using two different pitch gears on a shifter seems interesting but also risky.

The main thing I would be worried about if you reduced the rod diameter is the little shifty bit (4-40 screw in WCP dogs). SW stress analysis could make sure it's safe.