Double post, yes, I know.
I decided to redo the bow and stern of the ship. They now have been simplified down to 1 or 2 quads each. This decision was made upon realizing that if my ship had both forward-firing main guns and forward-facing fighterbays, whenever it lined up to fire its guns at an enemy, it lined the enemy up to fire its guns down its own fighterbay... which is a bad idea. Sure, in FS2 shooting the fighterbay doesn't (usually) do anything, but it would make a stupid design in real life. I removed the stern bay (and nearby greebles) because I am planning on placing the fighterbays in the previously useless ventral cavity.
Suggestions for what to do with the bow and stern, as well as with what is still boring polygons, would be useful.
Also, I would really like to see this finished! Post/PM/otherwise contact me if you are willing and able to assist.