That's what I'm going to do as well.
No pics yet, but I removed the trench "back wall" on the upper hull last night. Because fibers inserted in the trench above the halfway mark would interfere with the upper hull back wall. I simply took my side cutter and cut the wall off. I left a little bit at the nose for alignment purposes and then around the two side indentations. Those, along with the inner bracing will align the rear of the hulls along with the engine block.
The nice thing is that the upper hull does indeed rest directly on the trench detail parts. This allows the upper hull to still be glued completely to the lower hull. I'll again use the Testors Model Master liquid glue for that as I'll be able to run a bead down each side of the lower hull trench parts.
Oh, and I've decided to add remote control to my lights. The engines will be on a separate circuit, so I can dim the fibers while leaving the engines at full intensity.