trouble shooting my cat d330c

Have you checked fuel pressure under all conditions, does it drop when the misfire hapens?

Justin, since it's in a trencher the fuel tank might be lower than the fuel pump. If this is the original engine it should be an industrial arrangement. That said due to the variables in fuel tank location all industrial engines should have a fuel return line to constantly bleed any air picked up back to the tank. If you have one make sure it's clear.
Next thing does the engine run smoother under a load? If it does then remove the small oval cover over the front of the rack, up where the pump mounts to the drive. Cover is held on by two bolts 1/2" hex(5/16 NC)bolts. Take the cover off and hold a very short pencil against the end of the rack to check for and stop pulsations.
Come back with what you find.
Later Bob

Also on the fuel side, plumb in a 2 gal tank above the engine with a decent size pipe to the transfer pump then run it and see if the symptoms still persist. Have you tried running it with the fuel cap off/loose to validate that it's not drawing a vacuum in the tank. Last thing you can do is pressurize the tank and see if that effects any change (only a couple of psi - do it with the tank 1/4 full so that the air pressure is easier to maintain).
When it runs properly, is there noticeable smoke and if so, what color is it?

Cheers,
Neil.

Take loose the return line and put it in a can of clean fuel while running the engine. Might have to be a big can if you're going to do it for long! Watch for bubbles.

The old fuel lift lines can be worn enough where the ferrules are on them to allow air to enter. May have to seal with teflon tape wrapped on ferrule or just replace with hoses etc. \

The easy way to pressurize the tank is clamp a piece of inner tube over the filler spout of the tank which has the valve stem in it. Pump it up enough to bulge it out some.

Have you checked fuel pressure under all conditions, does it drop when the misfire hapens?

Justin, since it's in a trencher the fuel tank might be lower than the fuel pump. If this is the original engine it should be an industrial arrangement. That said due to the variables in fuel tank location all industrial engines should have a fuel return line to constantly bleed any air picked up back to the tank. If you have one make sure it's clear.
Next thing does the engine run smoother under a load? If it does then remove the small oval cover over the front of the rack, up where the pump mounts to the drive. Cover is held on by two bolts 1/2" hex(5/16 NC)bolts. Take the cover off and hold a very short pencil against the end of the rack to check for and stop pulsations.
Come back with what you find.
Later Bob

Also on the fuel side, plumb in a 2 gal tank above the engine with a decent size pipe to the transfer pump then run it and see if the symptoms still persist. Have you tried running it with the fuel cap off/loose to validate that it's not drawing a vacuum in the tank. Last thing you can do is pressurize the tank and see if that effects any change (only a couple of psi - do it with the tank 1/4 full so that the air pressure is easier to maintain).
When it runs properly, is there noticeable smoke and if so, what color is it?

Cheers,
Neil.

Seems you've tried all the obvious things.
You mention rebuilt engine. Irregular firing can be caused by the burning of excessive lubricating oil escaping past new rings which have not fully seated.