@grywitt Did you clean the engine off?
The cooling fins look brand new. (As in 24hrs new, so believe the hour meter.)
I think that getting really black oil out of an engine isn't super unusual- if it has a bunch of hours on it. The carbon never really comes out of the sumps in my experience. (So don't believe the hour meter)
That raises the question to me of how does one get a machine that runs at 1/2 its rated output (+/-) and has a bunch of carbon in the oil if this is a new engine? (Believe the hour meter)
The inconsistency that I see is that even though there is debris in various places in your unit, the fans and fins look really clean, as does the muffler insulation, wires, etc. To me, that argues for the hour meter is probably in the ball park. The oil argues for either much higher hours, or yes, something more serious like broken rings, or damaged valves or valve seats, or the valve guide seals are missing, or something like the decompression lever is always at least partially engaged, or there's half a rag behind the engine preheaters. I think that it is running too well for the camshaft not to be correctly aligned, but it might be possible. When you turn the engine over by hand, is it easy or hard to turn over? Without the decompression lever, this should be pretty darn stiff. If it is hard, I'd take the head off and look for foreign material.
No matter what, I'd button down the fuel lines first.
If you prime the set with the output of the Racor into a clear jar, can you see bubbles? Or do you have a segment of clear fuel line that could temporarily go between the last Tee fitting and the injection pump? It might be a quick test for bubbles. You may be looking for 1/16th inch sized bubbles, so I find a bright flashlight helps. If you find bubbles, I think that means hunting down the leak. If you have bubbles, if it were me, I would go from the tank to the injection pump and disassemble and clean the threads and barbs, checking for debris, and then use a good diesel thread sealant on the threads. Because this engine is so persnickety about air leaks, I prefer to use the style of hose clamps that don't have flat spots at the tightening mechanism. (I couldn't really see the defect that you were concerned about on the injector, but as you have clear hose, if it were me, I would lift the hose up and see if the bubbles accumulate, or move downstream.)
My bet at this point, if the compression is low, would be on broken rings, but I'd be open to something odd. Carbon issues in a twenty hour Yanmar is more than unusual, so something is amiss.
Sorry for the long post, but even if the engine were poorly fueled (overfueled), I have trouble spinning a scenario that lays all of the blame on an air leak and gets the oil to be that dirty, though the better performance on the segregated fuel return suggests that there is an air leak, even if it doesn't cause 100% of your issues. If it had just been SeaFoam, the subsequent test should have been better and they weren't.
