This might sound like a stupid suggestion but having gone through the same thing you describe (and having gone through the same electrical, ignition, timing, and fuel troubleshooting work trying to figure out it), my main cat was clogged and I couldn't get over a certain RPM while driving but it would free rev fine.
I felt like an idiot because it was so simple. If you have cats, check them if you can or simply drop the exhaust.
Edit: I even went so far as to sit on the engine and hold on for my life while my friend drove the car and I watched the on rail fuel pressure gauge. I was seriously running out of options. When you're willing to die to diagnose an issue, you know you've got problems...

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