I'm getting the black box of doom as well when I try this, just this mod loaded.
I can tell you why (I think) though. Your flagship_prototype_floor.png file isn't the correct size, it's 650x469 and should be 800x525. Your empty Gibs also have incorrect dimensions and are showing as black boxes. Replacing the flagship_prototype_floor.png with a correctly sized empty PNG fixed it for me.
I had a similar issue myself last night with a missing / incorrect floorplan giving me a big black box, so I knew where to look
I like the concept, I felt like a glass cannon which could annihilate things if I could survive that long. Since you have both the Nuke and the Glaive however they feel like they both kind of solve the same problem (long recharging doomsday weapon). Perhaps the Nuke could recharge and/or move slightly quicker but cost 3 or 4 missiles to deploy? (that said I did like it when I fired the Nuke but the Enemy FTLed the hell out of there before it hit
Really like the ship layout, especially the long corridors up to the weapons "nacelles" and the 1 person medibay supplemented by the Engi nanite heal.
Ship feels a little too high and to the right as well, maybe tweak its offset down a bit and left a tiny bit?