How do I stop Hader (Star Wolves 3)?

Yeah, most modding has to happen midgame - early game missions are more or less forced on you so you can't deviate, but after you get the repainted Mastiff you can start wandering around already. That's not to say you can't mod stuff earlier, you can mod even the starting tug you begin a new game with but obviously there's not much point in that since you lose it soon anyway.

Be aware that modding items which you already have can produce strange results - i.e. it's best to mod stuff you haven't got yet.