Jon_O, what a big read. Didn't want to post given the capable hands looking at it for you but this may be worth considering and I would try this first. Then try a very short run after dry rotation if the drag/roughness you feel is eliminated - rotating clockwise as you have done previously. Sorry this has become so long.

I just went through all the advice - as usual it cannot be faulted. The only ODD thing I can find is in one post you lodged to do with taking delivery of the vehicle back into your obviously capable hands. The wording you used in that post concerns me in that ".....the crank was aligned so I.....". I wonder if the crank locking pin was actually in the correct aperture of the flywheel.

You've probably run through all this but it seems you have checked everything else multiple times. Please forgive me if this is all to apparent to you.
Behind my thinking is this:
I began to think is she truly aligned at @ the 90 after mark? To be sure with #1 is @ TDC only rotating clockwise until you find that mark...this is From your words and storage of the injectors they do not seem all that capable nor diesel savvy. That could cause the knock I hear in the video and the issues you describe. I wonder if that noise that is more of a fluffing sound is not injector or to do with fuel but valve cross-over due to "just-off" engine timing.

There are some 6 or so holes at that pcd that could be found by the flywheel locating pin and one is only about 12 degrees after the correct hole. Whilst watching your video it seemed that the marks did not quite line up so with translation though the drive to that it could make sense. That could ostensibly advance the timing by the amount I see against those marks that look like the ones you've made.

In listening to and watching the video again the engine is timed off these two most recent timing marks (in blue/black marker) seeming to me to be a tad advanced (camshafts marks relative to backing plate marks) whilst RUNNING. My suggestion is it is [u]not[/u] out by a tooth at all (I know that hasn't been mentioned in the thread that I can recall) but it is just slightly advanced by the amount I rather poorly describe. The video is also demonstrating a distinct rhythmic fluffing noise in sync with its idle cycle when you isolate the normal noises like injector tick and other usual running noises. That implies to me that it is timed in advance by the said amount leading to valve overlap - slightly too early and beyond its ability for self-compensation - just. This is more likely to happen with a diesel engine as the cam diagrams are very much tighter than for a petrol engine as is the valve stroke much shorter than its gas counterpart. We are dealing with a lot of valves and the fluffing could be due to one valve only causing the overlap. I would need cam diagrams to work this out or to have a motor pulled down in front of me to predict which valves might be involved.

I actually think you have, at this stage, a false injector pump timing mark alignment, so it is misleading.
You are probably well aware of the following but:
You could try a noid light for the injector pulse but if you have an inductive timing light that may better serve your needs. It could be particularly useful for checking # 1 timing with the engine running if the front pulley is appropriately permanently etched so you can see it easily with the engine idling.
Before I do anything else to mine I plan on making a similar mark.

Also unnecessarily confirm the bracket is indeed for the alternator on the 06.
Hope that helps.
Good luck