Old post ,,but the letters were for the bore size. Yamaha used them to match a piston to the bore according to size referring to the letter on the cyl.
Funny thing is, is I have seen on other cyls (specificaly Yamaha watercraft) that are marked with similar lettering but that the lettering is for a grade in reference to how well the ports in the sleeve are matched to the aluminum in the actual cylinder.
Ex.. A "B" cyl is closer in alignment than say a "D" ..