Just something to consider...I have a 6.9 diesel in a 1985 F350.
I started hearing a thumping noise that I thought was a bearing going bad. A mechanic listened to it and said it was a bad injector.
I had my injectors rebuilt (cleaned and pop tested) had two cracked sleeves on the injectors.
I have just re-installed the injectors and started the engine, but because I have some bad leaks at the injector connection to the hard lines from the pump I haven't run the engine long enough to determine for positive if the sound is gone.
My truck is a VERY noisy diesel anyway.
You should at least consider your injectors.
The rebuilders that did my injectors ask me if my fuel was old.
It was VERY OLD as this truck has been down for years due to electrical
wiring problems (Fords short out in the wiring harness under the dash near the fuse box)
My fuel had varnished and I couldn't easily drain the tanks (they were very low, near empty) so I put an entire can of Seafoam in each tank to hopefully dissolve any junk in them. I put five gallons of new diesel in the one tank I run off of and started the truck using that fuel.
As soon as I fix the fuel leaks, I will put at least a half tank of new diesel in that tank and add Stanadyne injector cleaner in the fuel and run the truck until it's empty to see if it runs better.
You should do this even if you have checked you lifters. They might unstick along with anything else that is crudded up.