3406 DITA not firing on all cylinders

I think you found your problem. If your plungers are not pumping enough fuel the nozzles won't build up enough pressure to "crack". You may be able to just replace the 5 and 6 plungers and cure the problem. Pump won't have to come off for this, but it may be cam in pump that actuates plungers. Since the motor set up a while I bet they are stuck in the mostly up position. Without full stroke of plunger naturally you wouldn't get enough fuel. Which ever way you choose to go at least you are sure of the problem. That much difference is sure to cause a miss.

 

Did you keep the shims under the plungers exactly like they were. That is how they bench timed them at the factory. Even when replacing with new plungers you always reuse same shim pack.

 

Is there any smoke either black or grey that clears up when you crack number 6.

 

Stuck injector.

 

If you didn't disturb shims under plunger and lined the notch up on the scroll gear when you installed it. should be ok. An injector can cause a knock that will get you excited. You can swap 5and 6 injectors see if it moves or stays with the hole that will rule injector or plunger out. Most of time an injector will cause the knock but I have seen pumps do it as well. Hard to say with just putting plungers in those 2 holes if you had a dual fold problem or created a new one.

 

Nothing to running the overhead, that is easy part of those engines. I am kinda wondering if a shim dropped from 6 and you didn't notice it. By cracking line and knock goes away its fuel related. With engine sitting up could be injector, but could be plunger time as well.