I tried a bunch of things that took up a lot of time, but this actually seemed useful. To attach the forms to the L-brackets, I measured and marked the position, but when I pre-drilled I made a significantly oversized hole, and then attached with a screw and fender washer. With the screw tight but not over-cranked, I was able to adjust the form position in small increments pretty easily. Then when I was happy with everything I cranked it all down and added a second screw to lock it in.

That's a good technique.
When I first started building (canoes from the Moores' Canoecraft book) I used bolts for connections, with slightly oversize holes.
Nowadays, I use metal L-brackets and I align the 'primary' holes in the brackets (with thread or fishing line through the holes) before I start adding the molds, shimming the brackets as necessary. It's a bit 'fussy' to make sure that the thread isn't being deflected by an out-of-place bracket, but 10 or 15 minutes will see that stage finished.
The molds have a pilot hole drilled at the intersection of the WL and centerline, and a screw drives through the bracket hole into that mold pilot hole. The next step is to align the molds (removing twist) by using sticks on the centerlines and thread stretched end to end (or by eye, the thread just confirms it). At that point, the end forms are checked for alignment.
Once everything looks 'lined up' I add the 'confirmation screws' as Steve describes, and staple some scrap strips to the molds (diagonally) to lock things into place. The scraps are removed after the stripping gets going.
At that point, the mantra : "It's only a boat" comes into play. You would be amazed at the asymmetry in some commercial kayaks (which I discovered picking up patterns from a few) ; a few mm is nothing to worry about.

There must be dozens of ways of doing this, just for external strongback construction.