I am having the exact same problem. I found the single player mod the OP mentioned for changing the ships you use in the missions, and it works for the first part of the game, but after the mission where you have to protect Biranu Station from the Cardassians, and Admiral Lieu calls you back to Starbase 12 for a "special" assignment, my screen either goes black, but I can still select my crew, or it doesn't go black, and says normal, but in either case, my objectives list is suddenly empty and my "Set Course" list is also empty, so I can't proceed to Starbase 12 or do anything else. I'm just stuck.
Does anyone know how to fix this, or if there is another method for changing the ships used in single player?
I am playing version 1.1 with Foundation and a couple of downloaded ships & bridges.