Truck Cutting Out, Replaced CPS, Truck Missing

My girlfriend’s brother has a 1999 PSD. He said it was acting like it was going to die so I gave him a CPS to replace his with. He changed it and said it ran better, but it still feels like it is missing. I don’t think it is likely that two problems came up at the same time. He "misses" at all engine operating conditions, but mostly on acceleration. Sometimes when he "gets into it" it misses, and sometimes it doesn’t. Any ideas where we can take it from here? I have suggested taking the chip out to determine if the connection is bad. The rest of the truck is stock with exception to larger exhaust. Thanks!