The copper is from the thrust bearings on the crank. The crank is a short stroke unit that is surrounded by a floating triangle. On each of the three cylinders is cup which rides on a side of the triangle, a spring inside to keep the cup on the crank, and a piston (which looks like a valve, the "stem" is the piston, and the head is the "rod").
When the pressure regulator restricts the fuel to the cylinders, they can't travel all the way down to the crank. This is what controls the output, fuel starvation to the cylinders reduces the stroke of their pistons, pumping less fuel.
Those 3 freeze plugs are so they can machine the cup/cylinder bores. When the triangle is allowed to rotate out of position (normally by a cup stuck up in it's bore), the next revolution crams the vertex of the triangle up into a cup. Somthing has to give. BANG, shit busts off, and the freeze plugs push out by debris wedged in between the triangle and the case.
I've lost two pumps, and had the injectors tested afterwards. No problems. But certainly clean the rails throughly.
The reason the debris doesn't go out of the pump and into the rails, is because the high pressure side is somewhat isolated by small passages and is feed by gerotor pump from the tank, not the crankcase fluid which is for lubrication and is not pumped into the high pressure side.