Hard to say just by description, but as a young budding mechanic ... I broke more than I fixed, until I realized that's a bad business model and got my self into classes, and hung out with the older folks that knew way more than me.
Low to medium pitch, gaining pitch under load and speed is typically pinion to ring mesh. It might sound great on a lift but there is no load of the car weight on the bearings and etc. It is possible it is fine as is, but changes once vehicle is on its full curb weight and moving forward shows it could be bearings or other issues in the setup.
You did thorough work on diagnostics of the noise so balance of the peripherals is probably not it.
Things changed were TQ so is possibility easy to rule out but will have to pull trans to swap out.
Main two things I see is differential noise, or internal in trans.
To me and based on experience, it sounds like a differential setup issue, yet could also be slop in the trans. The internal total run-out is controlled by selective nylon washers and not a lot today understand how to setup an older TH350 or TH2004R/700R4. Engine RPM at 3,000 can easily have internal components at 20,000 RPM or more. This can produce the issue you are having.
Then also have to ask... Did you try rotate tires? Did tread style change? Tire with slipped belt?