Maybe this photo will help.
I shot a photo of the Norman White cylinder, next to my stock 650 cylinder, and put numbers next to all the holes.
The numbers in Pink, are the standard holes for all 650 cylinders. The numbers in Green, are shown on the Norman White cylinder only, and those are the recessed thru bolt holes for the Commando style thru bolts.
Photo here (sorry, I don't know how to post the photo in this thread):
http://i1228.photobucket.com/albums/ee4 ... gnpr08.png
On the photos, the Pink numbers 2, 5, 9 are thru holes for the studs that come out of the head.
All other Pink numbers, are the threaded holes. (Total of 10 holes which are standard Norton pattern - either threaded holes or thru holes)
Any hole that's not number is either the oil drain hole, a pushrod tunnel, or the holes for the pistons.
Hope this helps.