Another update.
I replaced the hard plastic fuel lines leading from the lift pump to the spin on filter, and from the spin on filter to the IP with standard fuel line and hose clamps. The bottom of the banjo bolt that connects to the IP was wet with clean fuel and so was the bottom of the lift pump, and one of the hard plastic lines looked melted(see photo). Edit: The photo looks dirty, that's actually pitted and melted. After replacing the clear lines, I have no more fuel wetness and as far as I can tell I have no more air in the system.
I pulled the fuel line from the surge tank to the lift pump off, stuck it in a coffee can, and turned on the electric in-tank pump. 3lb coffee can half full of fuel in less than 30 seconds. The lift pump is getting enough fuel.
I still have the miss, and some gnarly top end noise. Yanked the valve cover and re-verified that all my valves are set within spec.
I took another video and posted the link below. I would very much welcome any suggestions anyone has. I am out of ideas, my next step is taking it to a Mercedes shop for diagnoses.
Yota diesel irregular rattling - YouTube
Thanks everyone.