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That is probably unburned diesel mixed with carbon because that injector may not be spraying correctly. That could be your miss!

Are you still using known clean fuel in your can or did you hook it back up to the stock tank that could have bad fuel?

If it ran fine on that trip, then sluggish, then ok after changing it with a new filter except it has a miss, sounds like something in fuel was bad.

What plugged your filter all of a sudden on that trip when it started running poorly?

Are you running on biodiesel or #2 ULSD? Bio will clean gunk out of the tank and lines and plug filter. You may have to change filter a few times. I would try pouring some Seafoam into the tank with about five gallons of ULSD and see if that helps first. Sounds like it could have an injector or...