The Pal Park is in Kanto.
Genosect is only in Pokémon Black and White. Genosect didn't exist in Pokémon Soul Silver.
Crystal is a GEN:2 game while Latios is a GEN:3 pokemon. (so no)
No. That region is not included to the game so it doesnt exist.
a silver apricorn makes a GS ball in Pokemon HeartGold or SoulSilver.
No Pokemon does NOT exist and it won't because it's only a cartoon. It does exist in games though as well as tv
It doesn't exist yet in Pokemon Silver
There is no silph scope in Silver, as Lavender Tower doesn't exist anymore.
Missingno. only exist in red and blue.
It DOESN'T learn overheat. You can teach it but it doesn't learn it naturally.
Zoroark is a generation V pokemon, so it doesn't exist in Soul Silver.
Whirl Islands only exist in Gold, Silver, Crystal, HeartGold and SoulSilver.
Deoxys didn't exist when Pokemon Gold, Silver, and Crystal came out. If you meant HeartGold, then you'll need to migrate it or trade for it.
Genosect is only in Pokémon Black and White. Genosect didn't exist in Pokémon Soul Silver.
Crystal is a GEN:2 game while Latios is a GEN:3 pokemon. (so no)
Deoxys didn't exist in Pokemon Gold, Silver, or Crystal; because Pokemon Ruby, Sapphire, or Emerald weren't made back then. So there is no Deoxy's Meteor in Pokemon Gold.
I myself am not aware of this fact of finding Manaphy in Pokemon Silver, but my answer would be this cave you are looking for does not exist because Manaphy does not appear until Generation IV. If you are using cheats this answer is irrelivant.
No. That region is not included to the game so it doesnt exist.