1 - in theory, all damage formulas are the same in regular pokemon and in pokemmo.
2 - i imagine "effective stat" is just whatever is displayed on the pokemon's stat screen. plus temporary in-combat buffs.
as in, it's basically: double your base stat, add iv and ev bonuses, scale it to your level, then add nature bonus.
and then if you like, use swords dance in battle, that probably applies too, doubling your effective stat.
3 - if the objective is just getting the calculation result so you can play pvp, there already exists a tool for this that everyone uses.
https://calc.pokemonshowdown.com/
but if you're trying to manually do the math for some other project, then do be my guest.