Unfortunately, if you've already beaten him and saved your game afterword than he can't reappear again unless you completely restart your game over. However, you can still try and find someone who will want to trade for him (granted they will probably want something of equal value in return - like another legendary).
As for the Master Balls, there is only one main one in the game and it is located in Team Aqua/ Magma's headquarters before you go after Groudon and the world turns all bright and "sunny". If you missed it though I don't think that you can go back because the cave-hideout will be sealed. You have to get it when you go after the submarine. It's located amongst three other treasure 'balls', two of which are the pokemon Electrode. The only other way to get another Master Ball (without cheating or trading) is to win the lucky number draw at the in-game department store. This however is a very, VERY rare thing to do.
As a tip: the next time you challenge a pokemon that seems unusual like Rayquaza or Groudon that have their sprites outside of battle - not just a random encounter, or those with special music, try saving right before you go into battle with them. That way, if you lose or cause them to faint, you can just turn the system off, turn it back on and start over right where you last saved. Don't feel bad about it either. This is a technique almost everyone uses.
give the guy up above the best answer he pretty much explained everything