I've been following the percentage prescriptions in the CA WOD, only taking the percentage of the weight I'd LIKE my next PR to be rather than using my current PR (so, if my max back squat was 75, I'd use 80 or 83). I get worried about getting too far out there, though, I figure the percentage things are there for a reason. But that's because I developed the tendency to treat programming like it is a magical formula for which deviation will result in disaster (I am slowly getting over this, though).
As for the shoulder pain, I was having rotator cuff issues last week, and while it got better this workout it flared up a bit. It was weird, my entire shoulder was in pain when I put weight on it (like pressing or jerking), rather than just the usual spot in the front. As soon as the weight came off, the pain left and they feel pretty fine now.