You have boiled it down to lack of air in cylinders. If you had restricted fuel return it would not deliver excess fuel as the internals of pump equalize and the pumping plungers will not take on fuel. If you can verify no restrictions right up to the valves them selves with intake and exhaust manifolds off you can forget about that. Next thing would be valve lift and valve timing. You need to verify that the valve timing is correct following procedure in manual, I don't have it on that model. I did see one John Deere tractor that had absolutely no power, smoke was normal for a fully loaded engine and the problem was transmission was over filled about 10 galons, filling the wet clutch flywheel compartment and placed a heavy load on engine when speeded up. But, if you have heavy black smoke with a normal injection pump setting you are just not getting air. If pump is over fueled you could get heavy black smoke from some external load problem in transmission or hydraulics. Not that familiar with that model though.
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