As Larry suggests, the M103 is fussy about coolant quality. When I pulled the head off ours the gasket was badly corroded and was allowing oil from the oil feed at the rear corner into the water jacket. Fortunately nothing else was corroded. Maybe the gasket works as a sacrificial anode. In your case it appears you may have been getting coolant into #6 cylinder. The problems often occur back at this end, initially with oil leaking from the rear corner.
I can see what you meant with the EGR pipe, our Oz delivery does not have EGR so it was easy to pull the head and leave the inlet manifold in the car. Unlike you, I only removed the rocker shaft and camshaft and left the rest for the shop that did the head for me. They removed the valves, cleaned everything, crack tested the head and skimmed it to ensure it was flat. They then reassembled it with new stem seals but claimed it did not need guides (140,000km approx.). When I got it back everything looked like new. All this including the VRS gasket set cost me less than $400 AUD. Three years on now at 175,000km it is still perfect. Not a single leak nor any oil consumption.
Good luck with the rest of your overhaul.
107.023: 350SLC, 3-speed auto, icon gold, parchment MBtex (sold 2012 after 29 years ownership).
107.026: 500SLC, 4-speed auto, thistle green, green velour.
124.090: 300TE, 4-speed auto, arctic white, cream-beige MBtex.
201.028: 190E 2.3 Sportline, 5-speed manual, arctic white, blue leather.
201.028: 190E 2.3, 4-speed auto, blue-black, grey MBtex.
201.034: 190E 2.3-16, 5-speed manual, blue-black, black leather.