Have you measured compression? (I know, tougher on a diesel engine). Unless you shaved the head or somehow used a thinner head gasket, I don't know how it could be too high. I know that in gas cars, the camshaft used and its clocking (some timing-sets allow up to 7 settings on the timing sprockets) can change compression. The concern for racers is getting too high a compression (>200 psig) so the starter can't easily crank over the engine. Anyway, re-verify the valve timing marks. I added a 4 deg offset key in my two engines to get it perfect (or slightly advanced), to account for timing chain wear.

I set my two 300D's for 27 deg BTDC "start of injection". It can be a little tricky to measure it perfectly, and people here get too hung up on the "1 drop per sec" method. All you are trying to do is find the crank location where the #1 injection pump piston first closes the inlet valve to "start injection". It is a very sharp location, whether you count drops or not. Setting earlier than the spec 24 deg is supposed to give better performance at the expense of slightly more idle noise, but I didn't notice a difference.''

The youtube sounds like a normal idle to me. I doubt the noise is internal since bad rod or crank bearings usually give a deep sound. Yours sounds like normal combustion noise. The fuel can make a big difference. I notice a much quieter idle when I fuel with "renewable diesel", which claims a higher cetane rating. From 20 ft away when idling, you can barely tell the car is a diesel. When my daughter fueled with fossil diesel recently, the idle was noticeably louder. You are in CA, so can buy Propel's Diesel HPR or Union 76 R99. They are bio-based, but work in any diesel vehicle (no mod's needed). Union 76 stations that carry it have ad banners "Renewable Diesel" (or did).

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1984 & 1985 CA 300D's
1964 & 65 Mopar's - Valiant, Dart, Newport
1996 & 2002 Chrysler minivans