"should I add any other exercises since the pull and press are out, GHD? abs?"
Yes, feel free to add in other stuff provided you can do it (which seems you have a good idea of AND that allows you to train without screwing things up too much).
"Have you tried any high rep versions of your principles? Possibly 15,12,8 with xx %'s or would this be something I'd have to test for myself or abandon 531 and find a routine more BB style?" Yes, we have done a lot of stuff by simply altering the TM to fit our goals. We've done it a lot with women, too. (to account for the differences in rep ability)
I'm going to use this an example so don't feel like I'm calling you out or whatever people do when they read criticism designed to help them. If you want to squat 3 days/week, things have to change. You have to account for this - you can't have your cake and eat it too. I see this all the time in training and it drives me nuts. For example, here is ONE thing you can do to kind of get the best of both worlds. I would NOT do this all the time - one must periodize (program/plan) their training. I've had people want to do the main work AND BBB work 3 days/week. And they can't quite figure out why they shit the bed.
Squat - 5/3/1 work sets, shoot for a PR on last set
Squat - FSL, 5x5
Squat - FSL x Widowmaker
If you are not prepared to handle this, or are getting too sore, your prep work would be:
Monday - Squat: 5/3/1 work sets, shoot for PR on last set
Tuesday - FSL 5x5
Thursday - FSL 5x5
Friday - FSL 5x5
That is just an example.
I'd also recommend you getting a sled with a HARNESS (not a belt) and possibly a sled with the SSB attachment. If this shoulder is "life long" you may want to attack training with some different implements. Good luck - my shoulder is still torn up from an accident and I thought I had it bad. Keep the faith and train what is trainable.