I think that if you split the model in three single parts (cockpit, wings/cargo bay, engines) you may be able to make it fly as intended. The cockpit can be made into the 'command module MK1' to fool the game, the central part can be a tank without fuel, and using the decouplers of this mod you should be able to attach the big orange fuel tank (from wobbly rockets mod) and make it work. The engines are apart so you can make them liquid fuel engines and work as intended. Or you can try to just separate the cockpit and have the rest of the shuttle being an engine.