Rob,
The three holes are to mount the steel housing for the magneto q-coupling bearing race that Alan mentioned. Looks like this:
This one is a spare. Rusty on the face as you can see (hidden by the magneto), and the bearing race would need replacing (presses in); but you can have it for the cost of post if something better does not turn up. I will be in Brisbane early October so the post could be very cheap indeed!
As for the holes on the side of the timing case above the engine number; I do not think that is original. Probably someone's idea of an extra breather. The standard breather would be for pressure to exit with any surplus oil out the standpipe at the bottom of the timing chest. This led via a tube over to and dripped/blew on the primary chain.
-Doug