Any reason a combination of tank sizes and placements couldn't be used? If you're wanting to go full CNG, would you actually be removing the stock fuel tank? The space gained would allow for the mounting of some of the tanks there. Even if they had to be custom made to fit in the space, the cost of the custom build would most likely be recouped in little time with the later fuel cost savings.
If you then wanting to mount additional tanks on the roof, they wouldn't have to be as large or as numerous, although I would personally make absolutely sure that they were mounted as solidly as possible to prevent them from becoming "missiles" in accidents like you referred to earlier.