Yeah, I agree as well on the above. Nothing to really lose by trying some adjustments.
I think I would focus on the smoke screw above all else. If it were turned too far in I think it could contribute to the kind of behavior you have seen. The touchy throttle response and instantaneous smoke are the telltales on that I believe.
Agree that the lack of the turbo in the intake stream should make no difference in the particular symptoms your video showed. The engine is obviously overfueling and the unstable idle is due to the governor barely being able to keep fuel rates under control with the current settings. The big black clouds that occur pretty much immediately as soon as you touch the throttle reveal the fact that the turbo cannot really be part of the story. It happens faster than the turbo could ever respond so you couldn't rely on the turbo to "clean up" that smoke with more air.
Misadjustment of the LDA seems slightly more plausible as a partial factor, for example if the smoke screw is close to the right setting but the LDA is not performing its limiting job and thus the engine is able to access full fueling even when off-boost. (The LDA is meant to keep full fuel setting from being available except when turbo pressure is moving the LDA diaphragm.) However that wouldn't explain the unsteady idle speed, so it would be a partial contributing factor at best, if any factor at all.
Another thought I am having after again watching the behavior in the video: the hydraulic dampening circuit (not shown or described in the info above that is focused on adjustments that can be performed on the engine) could also be affecting the pump's ability to manage a stable RPM. It's meant to help avoid sudden or oscillating movements in the governor and is set only on the test bench, can't access it or really adjust it at all with the pump on the motor.
Two more good resources to add to the above that go into detail on that hydraulic dampening function, as well as all the other things the VE pump does.
https://www.dieselduck.info/machine/...ion%20Pump.pdf
https://injectionpumps.co.uk/pdf/bosch_ve_pumps.pdf
I still stand by my (perhaps pessimistic) assessment that you probably unfortunately bought an injection pump that was not calibrated correctly and it may need to get put on a proper Bosch test bench at the end of the day if you really want the engine to run at its best. The seat-of-the-pants adjustments you can make with the pump running the engine can help but will never reach perfect setting, especially since if you find that those are misadjusted it should make you presume that all the other bench settings you can't adjust in-situ (eg dynamic timing advance curve, hydraulic dampening, etc) are also wrong. But it is logical to try the adjustments you can get to before taking any further steps, even if for no other reason than to confirm the theory that pump miscalibration is the root of your problems. And who knows, maybe you will manage to get it to a satisfactory place just with those changes.
Let us know what you learn!