Bent rods #2 and #3.
The rods are more than likely very slightly bent causing your eratic vibration.
Causes:
- History of blown turbo. hydrolocked engine bending the #2 and #3 rods. The reason is that oil drains first into the inner cylinders due to the shape of the manifold.
- History of "Foam Piper Cross" air filter (water ingestion)
I know you can take a valid compression reading with the best of them, and the evidence points to rod damage.
The rods if bent won't necessarily fail, but they can exist with mild bending for a long time.
I'd say measure using a glow plug insert actual cylinder extension as you rotate to TDC.
Note the Degrees BTDC that the piston stops moving, and ATDC that it begins moving again. You can then bracket the approximate bending moment of the rods.
As the engines injectors age, the variation in compression will become more evident as the flow balance moves away from optimum. The crank acceleration may be close enough that the "Balance values" appear normal because of the +/- relationship of the sister cylinders being slowed due to the damaged cylinder crank acceleration differences... In other words its going to be really hard to see using Group 13 data.
Start with Rods, and measure piston extension.
My best guess with what little I know of the motor, but the symptoms fit.
Eliminate those and I'd start looking at a bad harmonic balancer or one that is out of balance or a brittle rubber bonding between the two metal sections.