sandstorm modifies the defender's defense before anything happens. pretty much this is applied directly.

pure/huge modifies whatever attacking stat is allowed by the ability's description, to the attack stat.

stat modifiers like attack/defense go before anything.

wonder room: makes all special moves do physical damage, and vice versa. "It replaces the identifier of the base special defense stat with the one for defense." Bad wording on this one to not include the opposite case.

to maintain linking compatibility with BW, nothing of the damage formula has changed.

I cannot find a place to discuss Damage Formula article, so some remarks:
Huge|Pure Power trigger description doesn't specify that the move should be physical.
Wonder Room trigger description implies all physical moves deal special damage and that's it, is it really true?
Sandstorm modifier description is not exactly clear: Is is chained with other multiplyers, or applyed directly?
And are there any known changes in BW2?