Hmm, thinking about this...
Wouldn't be particularly straight forward to do it with a plain square, would have to rig up a 't' square of some sort.
Either a small enough square to sit in the bore with a straight edge across the top or a straight edge on the cyl base with the square on top.
Better yet just a block of some kind in the bore (that's well squared up) with a straight edge on top, a cylinder turning or squish cutting mandrel would work nice but then chances are you've got a lathe.
Might get away with a 't' cut out of stiff card stock...
Could also check the squish band against the bore and then use a depth gauge from there to base if you were lucky enough that the band is close to spot on, likely not much chance of that though. Or do the math to compensate...
That said, I don't think I'd be comfortable with anything out side to side by more than sub .001", a little challenging to spot without precision stuff...
General rule of thumb I go by is if white light will shine through a gap, it's at least close to .001"or more, at .0005" or so it will shine blue-ish.