I wouldn't worry too much about locating pins, but clearly mark around the bolts to get them in exactly the right place.

You can get the 'box out by dropping the subframe on one side and lowering it on the other a good few turns.

You might also find it easier to get the balljoint out of the hub carrier after you've lowered the subframe a bit. Not tried it that way myself (just used a big fuck off pry bar) but it's meant to be easier that way.