I just want to clarify Fish Chains. Is it just Fishing in one spot with a Super rod while encountering the same Pokemon to build up your chain?
It can be any Rod, and you don't have to encounter the same Pokemon. Here's what you do:
Choose a spot to fish. Surf to that spot. Do not move from it - don't even change directions. You cannot move at all.
Fish repeatedly. Run away from the battles until you get a shiny. It usually takes about a chain of 40. You do not have to get the same Pokemon, and you do not have to use a certain Rod.
It helps a lot if you put a Pokemon with Suction Cups (Octillery or Inkay) at the front of your team.
Does playing a different version of the game on the same system give you a different friend safari or not?
When I tested it on my X version, I got Rock with Nosepass and Magcargo. I don't know my third one, because I haven't beaten the Elite Four yet.
The Friend Code is tied to the 3DS SYSTEM, not the game cartridge. Once you friend someone, they are friends with your SYSTEM, not your game. It doesn't matter if you put a different game in the 3DS, it won't change your Friend Safari type or Pokemon because the Friend Code has nothing to do with the game itself. I'd be willing to bet that you could even friend people who don't own X or Y and you could still encounter their Friend Safari.