Pat, the longer part of my strongback started out as a discarded (white ant attacked) laminated roof beam about 3' too short to which I glued another chunk of discarded timber and added side braces to extent to the required length and stiffness. Straightness and twist, or lack thereof, was not considered a priority.
Set up a builders string line [the yellow line] from the scrap pieces of ply at each end of the strongback and measured all vertical offsets from that string-line and used the small spirit level seen in the pic below to align everything vertically having drawn centrelines (just visible) on each frame and also drawn on a vertical offset reference line too.

Note that I added 20mm to all the vertical offset dimensions provided by Tom Yost to keep the string line 20mm [3/4" to the non-metricated] clear of the kayak frame to simplify all subsequent checks of frame alignment.
Had no problem at all with strongback or kayak frame alignment.
The ink centreline drawn down the strongback was only used to locate the upstand "forks" which, in turn, held the plywood frames in place; as stated above, ONLY the string line was used for alignment.

Hint: Were I to build another SoF, I would make taller "forks" to attach to the upper section of each ply frame as well - this would give better 'fixity' to the frames when fitting the chines and inwales..