I have also seen a fair few different of these marks and in doing some measuring and talking to John Underhill i can confirm that they are measurements from the base of the cylinder skirt to the top of the combustion chamber.
For example : F5 49 64 is actually The Designation ‘f’ (maybe flyer?) then
5 49/64″ (5.7656″) . Correspondingly 5 7/8″(5.875″) is the height for the other one.
I have a SS 600 barrel bored to withing an inch of its life which has the Designation HC (high compression?) 5 11/16″ (5.6875″) as well as a 5 5/8″ (5.625″) block which is a SS 500.
Also we have a SS500 designated as F 5 13/16″ (5.8125″) and also a L/S 600 blind block with 5 27/64″ (5.4219″) ..
so a whole bunch of possibilities!
They dont appear on all blind head (twin exhaust port) blocks ive seen but there are a lot that have probably been covered by remedial work for frost damage.
I have also measured a few barrels up to measure port timings to confirm their identities and the SS blocks i have tend to measure about 2.750″ (2 3/4″) from the base of the skirt to the top of the exhaust port and the long strokes around 2.9375 (2 15/16″)
The Short stroke engines have shorter rods, but the pistons, though the same distance between the skirt base and the pin centres as the long stroke type, have about 1/16″ more length in the area between the pin and the rings. This makes the rings and the overall height of the piston 1/16″ higher on a shortstroke.
This is my observation and indeed the difference between the top ring land edge(which is effectively the crucial point for port timings .. is quite often (but not always!) insignificant between the two types.
hope this helps..