Hi Danny. As far as the consensus on not getting stuck down low/hips/out the back that is pretty standard teaching in a Masters environment for 2016. Back in my early days fly was a lot different. It was a one kick per stroke cycle approach with more glide and a longer pull. Too long. The big differences in today's fly vs. 30 years ago.
1. Catch early and finish that pull insweep at the latest by the chest. This is not where you want to translate TI's minimal stroke counting. Rhythm rhythm rhythm and the rest will take care of itself. If you get to where you are competent and rhythm kicks in it's ok to be aware of your stroke count, but don't make it some kind of goal. Remember you inherently have a lot more time to slow down with both arms in use at the same time where freestyle has alternating arms to keep propulsion up. Fly is about finding rhythm.
2. Kick your hands in and kick your hands out or close to that timing.
3. 'Chase' down the pool towards the wall or in other words less up and down, more forward.
With someone in your scenario and a bad shoulder I'd especially like to see you cutting your pull off a little early than even a fraction late. You will get the timing down with more and more practice, but will hopefully find that happy place where rhythm takes over. Fly isn't a muscle stroke it's a rhythm stroke. If it's feeling as if you are Atlas with the world on your back time to pull the plug and start over.