One of the greatest advantages you have against any boss is that you, unlike the bosses, can heal. So, just pack a bunch of oran berries for future bosses, now that you've killed Moltres.
well, i have a guide, and it says........ he's at lv.42 and with 400 hp. if ur a grass type, use ranged attacks like bullet seed. when u recruit moltres(after youve beaten the game) he'll be at lv.52