The most common problem with cutting the head too much was that the timing chain becomes too long and is hard to tention.
I have heard of people shimming the cam towers but never the head itself. I doubt that valve clearance to pistons will be a problem. The head has a minimum thickness and if more than a mm has been removed then it has been exceeded. I would measure and check against the spec. If you are within .010in of the standard I wouldn't worry, put it together.
But, figuring that you are rebuilding the whole thing I would really worry about using a head that had a seat drop. That only happens after extremely overheating and with the thickness problem you are risking a bunch by reusing it.
Bosch Master, ASE Master, L1
33 years MB technician