A couple of ideas from re-reading everything again.
You made a pump gasket. Then I read you bought a JD one.
Is it possible to assemble any of the valves backward?
Pressure check point=90-160 psi to start and dropped to 0 psi after a few shifts of the HLR. When the pressure dropped to 0 at the check point the inlet line pressure remained at 60 psi and the outlet at 0.
Why is there pressure at the cooler inlet, yet none at the transmission test point? At speed, the pump is pushing out a gallon every 6 seconds, it gotta be going somewhere
If the clutch lube valve was stuck in the up (bypass) position or the spring was broken the oil would vent straight into the case and no pressure would be present at the cooler return line. The pressure would be 0 and there would minimal flow toward the cooler. Does this sound correct?
Yes. The cooler bypass valve is a compensating design though; it should produce about a 60 - 80 (58-72) psi differential. With the clutch lube circuit at 0 psi, the bypass valve appears to be operating correctly.
What if the cooler bypass valve was plugged on the inlet side? There would be no pressure on the return line or to the clutch lube circuit.
If the bypass is plugged, wouldn't that increase pressure on the cooler and the clutches?
You mention a buzzing noise. In the cacophony mine makes, I do not hear a buzz from the transmission. One of the valves vibrating? Broken spring? Pulsations from the pump? The cooler bypass and the pressure regulator would be the ones under high pressure.