Harley, Brent.
I did grind both sides. From my random 'granite block' encounters, If I found a 'good/uncracked/unrepaired' housing, I more often than not found small undulated uneven ness but small in nature. (.001 - .002"). Because the block side is the largest in 'diameter', I sat it on the Blanchard table and looked for even the minutest gap with a feeler gauge and using misc. assorted feeler gauges I would put them in the gaps. I found that the grinder that was accessible to me had a strong enough magnet that it would pull down hard enough to erase the gaps if I did not reinforce them. By inserting the feeler gauges my feeling was that the top side would not be under any stress when grinding the top side. In doing it this way, I felt that when turned over, that side was flat with no stresses and subsequent grinding could be counted on to be both flat and parallel and stress free.
I have only done this nine times because I am not a 'motor' man, but after the first six times doing it this way, I have quite checking altogether (when using the .012" grocery bags paper). For the reason that Brett states, I do NOT use sealant of any kind as well.
Again, just as a side note: If you are not doing this for 'Fine Point' or specific about originality, just buy two similar lower gaskets and cut the upper 'shims' from the same gasket material. ALL the bolts are the same size equating to the same torque. Once you feel that you have addressed the housing flatness, this should be a no-brainer for the shim issue.
Again, just thoughts from an old man!