The graphs tell a story, but it's not the one you think.
The first problem is that you don't have enough data points here to regard these things as trends. Your squatting graph contains 26 data points over 3+ years. Your 1RM BS/FS/DL/P contains 24 points over the same period. When you consider this small number of points occurs over a large period and within a 3/1 scheme, you can't explain anything here. You had a difference of 80 pounds on 5RM squats. That could be due to fatigue, poor planning, no warmup, hangover, rickets, day after FGB, whatever. Not descriptive.
Second, and more importantly, you don't have enough F'n data points PERIOD! You plotted 12 points where you did a 5RM squat over a 3-year period. A novice does that in 4 weeks of linear progression. You stretched a month into three years. No wonder you're not getting stronger.
Finally, that graph is exactly what I'd expect from unsupervised CF training (I say unsupervised because there are some good CF trainers out there). Going along and throwing some strength movements in there doesn't get it done.
Your benchmarks aren't bad for a guy your size (other than Elizabeth; you need more power endurance).
Your questions (my comments in bold):
1) What do I need to do to be a better Crossfitter?
Stop crossfitting for a bit and get stronger. You need to eat at least 50g more protein to do this.
2) Has anyone seen this type of shoulder girdle issue significantly impact all lifts?
Yes. Prehab, rehab, and do mobility work on the joint. My shoulders are messed up, too. It's our cross to bear.
3) What am I not thinking of that could be a factor?
You get better at what you practice, pure and simple. If you practice everything, you get a little better at everything, assuming you practice it well. There is something missing, and it's strength and/or coaching. Practice getting strong and practice performing the lifts properly and conditioning at the proper frequency and intensity.
4) In short, what the f*@% is going on?
Hard to say without seeing you.
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