I am sure you have tried/checked these, but I didn't see them mentioned above.
1: Are the u-joints in phase with each other? Meaning, the slip yoke can come off, and depending on how many spines it has, can be slide on in many ways. But it MUST be slid on so that the u-joint is in phase with the other u-joint. See image below, even if one spline off, it can cause some nasty vibrations.
2: You did mention having a CV and shims in back. So does this mean the rear u-joint is at roughly zero degrees, and the CV is taking up all the angle?
Assuming the top two items are not the issue. If it was me, I would stick my GoPro under there, probably on three trips, pointing it at different spots, and set it to the highest frame rate it can do, so I can easily play it back in slow motion. I have solved many issues with this method before.
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