I am sure more people than me have seen in the pics exactly where it was coming into the cylinder in the last set of pictures. I can see the gasket material is a bit different in the path from the water jacket hole and the cylinder, I would be sure to check in that area the most for any warping issue. Every time a shop pulls a head off an engine for a head gasket, Myself, Or another shop, It is always properly checked for the block warping, and the head is machined flat to be sure the problem does not happen again. I do just about 3 of the Ford f series from 03-07 with the 6.0 diesel engine a month at the shop I work for (engines known for horribly warped heads and blocks from poorly designed engines and head gaskets) The best way to have a good piece of mind is to do it right the first time! I hope it was just time for a head gasket and you don't run into this problem in the future when it is all said and done!