I would strongly suggest removing the egr tube where you can clean it out real good at the intake manifold end. That is where you will see the majority of the build up.
Paul - when I recently replaced my head gasket I did not take it to the machine shop for cleaning/prep work. I am not using oil and did not see anything that alerted me that it needed machine work. My intentions are to run it closer to 200k miles before any machine work. How much did they remove from the head surface?