you cannot change game files or change npc behaviour. the game won't run if you change files. this reloading problem is only in the very beginning of the game. once you get access to stronger weapons, the problem will become smaller and smaller. try to kill enemies 1 by 1, just shoot them with everything you have. after mission 2, you can also go to prison in texas and sell the pods. until then, best way to level up is trading in new york system