You did say,... you were doing this off memory.
I would like to suggest, in the nicest possible way,.. NOT doing this off memory.

Measuring the diameter of the bore down to 0.001 of a millimeter seems over-accurate to me.
At that level I would expect to see some variation in the bore from top to bottom, at least.
Did you measure the bores in a few places? If so, was there any variation?

So lets just say you have bores of 54.01 and used 'C' pistons of 53.95.
Assuming that these are standard Honda pistons and that you made the measurements 15mm up from the bottom of the piston skirt,..
Then this gives you a piston to bore clearance of 0.06mm.
Honda recommend a piston to bore clearance of 0.035 to 0.044mm with a service limit of 0.08mm

I guess this means that your 'C' pistons (if measured as assumed) are out of spec, but not outside the service limit.
So you could potentially use them if you wanted, but,..
the arguments for and against doing so will vary depending on your specific situation and thinking.

Me,.. personally,.. I would buy some new pistons.
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[color=#808080][size=9]Yes,.. I too know how to waste Time and Money,...