Perhaps you could add tweakscale functionality? Like, if you make the warp drive smaller/larger using tweakscale, the warp bubble will become smaller/bigger too?
You need a big lifting stage(s). On another note, whenever I tried to fire up the main engine to move the IXS the ship would start flipping out, and it would not stop turning with the engine on, even at minimal power. Any ideas on how to fix this?