Some filters for diesel application have chemicals in them (called supplemental coolant additive) to prevent cavitation, but filters are also available with no SCA (NAPA #4070 or equivalent.) I have one of those on my 7.3L. Once it filters out the initial casting sand, etc. they come out pretty clean when changed out.
It sounds like you might need to do a pretty aggressive flush like Jon G did. The rear of the block gets pretty gunked up. When I first got my engine, i pulled all the core plugs and scraped out whatever gunk I could, then went at it with a pressure washer. The rear plug behind the bell housing was nearly filled with gunk.
