Running on diesel clean killing the knock means it's not a rod, you're free and clear there.

Definitely kill injectors one by one and see if you can localize the knock to one or two cylinders.

If your injection timing is good, injectors are good, valves adjusted properly + reasonable compression, and cam timing is good, and lift pump is good(supplying proper pressure to your IP)................

Have you driven it? Does the noise go away above a very certain throttle setting? Do you have to drive it in kind of a binary manner to avoid the noise, either on or off?

I don't want to beat the delivery valve seals drum too hard just because that's what my issue turned out to be, but man I chased a similar noise around my engine for two years. I fixed all that stuff above(which should be done anyway), but replacing the delivery valve seals solved the issue. Wish I had known back then, five bucks in parts and well under an hour to do the job would have saved me so many headaches. Other threads here on the forum lead me to believe that this is a fairly common problem.

So yeah, throwing it out there. Nice clean swap, looking forward to seeing it drive.

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617 swapped Toyota Pickup, 22-24 MPG, 50k miles on swap