I was seriously planning to, then it was getting towards the end of the summer and I really didn't want to overcomplicate the build and possibly missing out on the rest of the season.

John has a tutorial and a video on it, you'll just have to figure out your spacing.  I also designed knees for the bow and stern transoms with cardboard for the inwales to die into.

Yes - I finished my spacered inwhales about a month ago and am looking forward (?) to a winter of sanding my boat.

I struggled a little bit with the guidance too, particularly since it doesn't directly address the Passagemaker and spends a lot of time focused on the nose-piece that we don't have. 

Some guidance I can give: I used 2 1/8" blocks with 3" spacers in between. No magic to it; that just looked right to me. The key seemed to be to make sure you have blocks on top of the two bulkhead dividers.

I "only" had about 20 clamps and for the blocks, I had read a tip somewhere on the forums about using an air nailer to tack the blocks into place while the epoxy dries. So I cheated, did that, and was glad I did. For the first set of gunwhale boards, I only used clamps, just started at one end and made sure I had good contact with the blocks all the way down. 

While I was waiting for epoxy to dry, I was inventorying what CLC boat parts I had scattered around my shop. That's when I found the 4 end pieces for the spacered gunwhales and figured out what they were ( I think those may be the knees that CaptainSkully identified above). Since the manual is for a skerry (I think), those Passagemaker specific parts weren't shown. For anyone wondering what they are: the parts are 4-6 inches long, have lots of angles on them, are made of the same wood as the gunwhales, and they fit perfectly into the inside bow and stern... once you know to try them there.

I was worried about installing these going in - the manual made it seem kind of risky - but looking back now, it wasn't really that hard. There's some opportunity to screw up, but that's true for the rest of the construction too.

Hope that helps some.