if the gas donor is a 8 lug 3/4 ton or 1 ton, it will likely have the NV4500, and that would be the best, as that is the same transmission as what the 6.5L would have had.
if a half ton, it would have the NV3500, which would be OK if you babied it and never pulled, but would not be a great idea.
Back to the NV4500.
If comparing same year gas and diesel, there are no changes. the changes are based on year, not on fuel type. if you sell the truck, it would do the next owner good if you could keep the swap limited to the correct year ranges, 96 and up had the internal slave bellhousing, and the 95 and older has the external slave. 92-95 only fit the external slave bellhousing, and 96+ only fit the internal slave bellhousing, so pick your transmission wisely.
mid 94+ has the better top cover with the 4 bolt removeable stub, which is a far superior top cover.
Good luck!