I agree with all your conclusions. The backlash isn't the main problem.
The only thing that would get worse the higher you go seems like it would be z axis related. Other posters have had issues where the z axis kind of wobbles even with a slightly misconnected coupler. This would explain it printing find for the first 1mm or so but if this is the actually problem it should get good again around height of 3mm.
I know you said you tested this. But maybe you didn't test it at 1mm off the bed? Maybe it's difficult to measure?
1) To test for this I would print something taller than the height of the threads on the z axis. Print a 10mm on a side hollow cube. Print it fast and hot: 240C, 100mm/sec, .2mm layers. Make sure you print the full 10mm height. Does the problem come and go 2 or 3 times as you go up the side of the cube?
The above test would also check to see if something is non-linear. For example maybe the bed tilts funny at the 1.5mm mark. For example if something is hitting the bed or pushing on it or something. But as you keep moving the z axis it should get better again eventually.
Theory 2 is underextrusion. But what the hell? How could it work fine for 4 or more layers and then start to go bad?
Check teeth marks? (like illuminarti suggests)
Bad temp sensor? (maybe the temp sensor is off and your print head is actually at 150C and you don't know it?)
Stepper gets too hot? (maybe after the extruder stepper gets up to a certain temperature it gets too hot and starts missing steps???) You could test for this by swapping the stepper maybe? And swapping the driver for extruder with x or y driver.
Try pulling on the filament while printing both near the bottom when things are good and again when things are bad. What I mean is fight the extruder, try to keep it from extruding. When things are marginal you should be able to prevent it from working. When it's printing fine you should not be able to.
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illuminarti 18
Take a look at your filament when it starts going wrong... and look at the teeth mark spacing (as discussed here...). Are you seeing reduced spacing, or other problems perhaps related to over-aggressive retraction? Whether that is the cause or the effect would still be open to debate, but it might at least give you a way to quantify the effect that you are seeing.
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