Didn't you get a SSB? Why aren't you using that?
If your shoulders are bothering you that bad you need to learn to alternate you ME pressing with your ME squatting. That way your shoulders take much less of a beating.
That last WOD should actually have been a relief on your shoulders. Start doing more turkish get ups and rollovers/armbars (whatever you call them). You need to be doing a lot of band pull aparts and face pulls as well.