small holes over the exhaust.

Yes. the small holes go above the exhaust port................. and one of the small sets of holes should be under the water outlet from the head.  The orientation of the gasket in the picture is correct. 

If the large hole in the gasket on the left front is placed on the right front, it can cause  the bridge between the left side exhaust port and the left transfer port to overheat and cause a piston seizure to occur in that area.