1. You had surgery on your shoulder.
2. You have spent a year getting back to some level of swim shape.
3. It hurts when you swim a lot, and your DOCTOR (the one who saw the inside of your shoulder and did the fixing) said if you keep it up you are going to re-tear it. YOUR DOCTOR told you to swim a lot less (every 3 days)---and to focus on events with very short swims.
4. Now you are asking the internets if you can STILL train for the 70.3 by swimming EVERY OTHER DAY (still not the recommendation from your doctor).
I just wonder if my expectations of what I was going to be able to do swim wise after the surgery are unrealistic or if I should get a second opinion.
I don't know about what your expectations WERE. But, given the advice of the guy who actually did the cutting and fixing...it sounds like they currently ARE unrealistic.
Perhaps, if you follow your doctors instructions, eventually the scar tissue, and whatever will slowly strengthen and allow you to swim more year over year. And, maybe next year you can swim 1500 yards 3-4 days a week. Take a longer view.