Ok, due to some strong suggestions about sep mode for this ship, as well as concerns over the proper application of damage textures, I have decided to create a proposal for this ship in sep mode.
It was very difficult to turn this ship into a sep ship. First, the ships shape was not condusive to hide two warp nacelles in the lower sep ship. I tried creating nacelles that would fit in the two "tails" on the back of the dorsal sep module, but its angle made that almost impossible. So I decided to just give the "tails" a warp plasma vent. The lower ship would not have a bussard ramscoop.
My second problem was getting both sep ships to look acceptable in form and function. I couldnt just flatten out the bottom of the ventral set ship....the head on the ship is already thin as it is, and thinning it out even more looked very strange. So, I created an indentation that the bottom of the ventral ships hull would sit in....this of course created a deep set of walls and a trench on the dorsal sep ship, but I think it still works.
Here is a quick and dirty example of what the ship would look like seperated. Note, the mini-deflector on the ventral hull is not illuminated, and neither are the warp vents on the dorsal ship. This is just a few pics to give you an idea how it would look.