So I just went through this a couple of weeks ago for my PMD.  I also happen to be a rigger, so I try to think outside the box, especially when the build manual leaves a bit to be desired on the rigging aspect.  Full disclosure, I chose the gunter-sloop rig option and built my own wooden mast, but I think a lot still crosses over even if you chose the lug rig option.

To determine where to drill the yard, I actually used the sail as the story pole.  I knew that the throat and the peak would need to be drilled as far out towards the ends as structurally possible to keep the head in tension.  Then I used the sail (that I just made) to determine where to drill the lacing points directly adjacent to the spur grommets built into the sail.

In order to avoid as many wrinkles in your sail as possible, you'll want all edges and corners under as much tension as possible, so all lashing/lacing will be "outward".  

I'm planning on doing a full write-up for the rigging of my PMD, but I wanted to answer your post ASAP.  I actually drilled a larger hole on the flats (same direction as lacing holes) 3/4 away from the direction of the halyard at the widest point of the yard and installed a soft shackle through that hole, through which I can attach a snap shackle on the main halyard.  This goes against the manual, but I percolated on this particular aspect of the rigging for weeks and this was the strongest/simplest solution I could come up with.  I'm willing to revisit this solution as needed.

Let me know if you have any further questions and I'll do my best to answer/post pics the next time I have some time off to rig the boat.  It's already started raining here in the PNW.  Hope this helps...

Thanks for your reply, Cap'n!

I have actually already drilled the halyard hole in the yard as described in the manual (which was terrifying as I'm famous for not drilling particularly straight...)

It's the hole (?holes?) in the yard near the jaws that's needed to lash the throat of the sail to the yard that's confusing me...

P