Two guidelines, 1) if a Pokemon faints in battle it is considered dead and must be released - 2) In each new area you're only allow to catch the first pokemon you see, if it runs or you kill it? Too bad
You are not allowed to use healing of any sorts (Stimpacks, regeneration, doctors, sleep, etc.), no Rad-Away, no Buffout, no healing of your limbs limbs, and any addiction you sustain cannot be cured