The box is one of the most important ship objects in UE. Remember mission 2b, with the big battle where capships fire dozens of torpedoes at each other? Well, capships can't fire torpedoes.
If it's asking for a .rom file, it's because it needs one. A .rom file is a room (in this case, the Dauntless CIC room); all missions that consist of more than spaceflight (so, the intro is an exception) must specify which rooms they use. If the game doesn't find a room that it needs for the next mission, it will of course crash.
Gun data is stored in bullet.iff. But you don't need the viper anyway - the Scims in Daniels' squadron onboard the Dauntless are the only Militia ships equipped with vipers at this time.