Charles:
I had similar issues with my Great Auk in getting everything lined up to the point where I was satisfied. Here are the steps I took:

First, I traced each of the lines on the patterns in a different color (Sheer in green, waterline in blue, etc.) It just helped make everything a bit clearer. I also made sure the lines on my strongback were long enough to be visible from either side of the form.

Second, I made a couple of wooden "L" brackets out of scrap 1 x 4 pine. I used spring clamps to hold the "L" to the strongback and the form to the "L". It allowed me to be able to easily move around the forms until I was happy with the fit. I aligned the top of the "L" with the centerline of the strongback hole on the form and used that edge to line up with the line on the strongback.

Once I screwed in the top cleat, I made sure the alignment was still good, then put in a couple of brads from my nail gun to hold it in place (I was having problems with the forms going out of alignment when I used screws). I then attached the side cleat, checked alignment once more and put in a couple of more brads. At the end, I checked the alignment of all of the forms, made whatever tweaks were required, and put in more brads to hold it all secure.

I have had no problems with alignment, or shifting forms.

Good luck. The fun is just starting.

Marcel