Not sure on the vibration, that could be engine/trans mount which I am sure you have already checked.
Did you set timing as per the FSM with the SST?
Bad crank bearings can cause a knock.
Piston slap can cause a knock too but it is generally not as pronounced.
It is always hard to troubleshoot here vs in person. Seems you are experienced enough though to not confuse say injector knock vs an actual pronounced knock.
We have repaired a number of 1HDTs where they got a bunch of boost added to them with nothing else done. Chowed turbos, blown head gaskets, ect. We have also seen crappy rebuilds with bores shaped all out of whack and ring gaps way off. So we tend to go through it all on the diesel builds when adding increased boost. 1HDTs are also known to lift heads with increased boost. That is solved with ARPs.
If you can’t narrow it down pulling the engine may be needed. If you got lucky you could get away with fresh rings, crank bearings and the ARPs along with a fresh OEM MLS head gasket. That is not to bad $$$ wise since you have fresh turbo, injection pump, injectors, flywheel, clutch, ect.
I have driven to Panama and back three times. If it was me and I was going to be living out of the Cruiser, going remote, ect I would want to know it is rock solid. You have got the FSM so you can see what is involved and it appears you have the skills to do it all yourself.
Cheers