Well I'm no expert... because I didn't remove the EGR valve... and I didn't remove the breather box.

Removing the EGR valve looked to be very difficult... mostly because the threads to the large aluminum pipes seem totally blasted by heat and corrosion.

Removing the breather box isn't totally necesarry... instead one can either pour some engine degreaser through the top of the box as detailed in the FAQ section during an oil change... or else just clean everything else about the flame trap system that can be removed. Cleaning that tiny pipe at the top that connects the input manifold to the 'Y' pipe going into the top of the breather box is the most important! Ream that out with a wire... or else replace it.

I scoured the brickboard for information about removing the EGR valve... and came up with very little. There were a couple posts about people in the same situation... who didn't report back what happened. It's sort of an unexplored procedure I think. Anyhow, my EGR valve seems to be working okay... so I left it alone.

Good luck!