To get another groudon/kyogre, simply edit your save file's name to that of another version. And open that version rom to open the save file. When you get into the cave again and aviod the Mt. man, you will see another legend. Then go to the Oak's place with groudon and Kyogre, you will get the GREEN ORB.
To get the Beldum from Steven ( or Daigo), you shall go to the Silph Bldg to meet him.
WHAT I CARE MOST IS HOW TO ACTIVATE THE LATIAS/ LATIOS PLOT ( Again, the Crystal is just a item, the key to activate this plot is to find the person who will give you the crystal, I think )