The first post of the following thread shows the method I used to clean up the manifold side of the engine using a plate to protect the ports during degreasing and pressure washing..
http://www.peachparts.com/shopforum/diesel-discussion/322334-engine-cleanup.html
My ports were not nearly that bad so I elected to leave them be, rather than risk getting a bunch of gunk into the engine.
I'd guess loose nuts on the manifold would be a significant contributor to the mess, but the EGR and the PCV probably contribute as well. You might want to consider a catch can too.