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Did you get a check engine light or were there any codes retrieved after the smoke started?
Did you seem to lose any coolant when this happened?
Was this with the original head?
What about the new head?
A machine shop should be able to do this, if the one you have dealt with cannot, maybe they can reccomend one.
If those cylinders were not firing correctly, that could be fuel or it could engine oil pulled into cylinder when it was not firing, or a combination of both. By firing I mean a lack of combustion or complete combustion in the cylinder which could be caused by coolant entering the combustion chamber.
I wish I could give you a more definative answer, but I can only use the info you gave me and it is difficult when you cannot see it for yourself..
I think it is from either coolant or oil getting into the combustion chamber due to a defect in the head or the head gasket. The defect may get worse as the cylinder head heats up or the problem developed soon after the repair. I have to speculate here as I cannot examine it myself.
This is the best I can offer based on your information. If you like I will opt out and see if anyone else has any input.