Answer to your questions:
1) Yes you can edit that without changing your odds. Just different PIDs now will result in a shiny Pokémon then with a different ID and SID combo.
2) Yes that is legal and can be obtained through normal game play. Though the combo will look suspicious to other people who might look at the data of the Pokémon.
3) Yes you can get shiny Pokémon through normal means and will only effect which PIDs will result in a shiny Pokémon.