OK, I just want to throw a bit of perspective on this:

Cylinders:
The difference in diameter of A -> B -> C cylinders is 0.015mm (54.015 -> 54.000)
The amount of wear on the cylinders required to hit the service limit is 0.07mm (54.085 -> 54.075)
(This probably has to do with the thickness of the nikosil coating)
Note that the wear limit of 0.07mm is much larger than the 0.015mm difference in cylinder bore size from A to C.

Pistons:
I don't have exact figures for new piston sizes but, going off the info you posted above and using common sense, lets just say that,
The difference in diameter of B -> Blank -> D pistons is 0.015mm (53.965 -> 53.950) This should be pretty close I hope?
The amount of wear on the pistons required to hit the service limit is approx 0.02mm (53.945 -> 53.930) Again, this should be pretty close I hope?
Note that the wear limit of 0.02mm is comparable to the 0.015mm difference in piston size from B -> Blank -> D.

So for a man who is used to working on Vespas, it would probably seem that Honda are being pretty 'finniky' about the piston wear, given the allowable cylinder wear.
Perhaps there is a good reason for this? I do not know how to explain this one.

But, what is important here is the piston to bore clearance.
It seems that a minimum piston to bore clearance of 0.05 is required.
On the large side: 54.015 - 53.965 = 0.05
On the small side: 54.000 - 53.950 = 0.05
Note: this is true for when the piston measurement is taken 15mm up from the bottom of the skirt.

Now I know that I have already quoted Honda as recommending a piston to bore clearance of 0.035mm to 0.044mm with a service limit of 0.08mm
So, assuming that we are on a budget here, trying to re-use old pistons, I am going to hack that statement and just say that we want,
A piston to bore clearance of 0.05mm with a service limit of 0.08mm

Your C barrels have worn a bit so as to effectively now be B barrels at 54.01mm (close enough) The nikosil will still be thick enough given the 0.07mm wear limit I assume.
Your D pistons measure up at 53.93 giving a piston to bore clerance of 0.08 (right on the service limit)
Your other pistons (from A and B barrels) measure up at 53.95 giving a piston to bore clearance of 0.06 which is not too bad if on a budget.

So basically, I will just say the same thing again:
You could potentially use them (the pistons from the A and B barrels) 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 (blank) pistons for what are now effectively B barrels.


Regarding the piston slap.
I have found that the noise is loudest when cold and reduces as the engine warms up.
It sounds like a semi-muted kind of clacking? That's the best I can come up with anyway.
Perhaps replace gudgeon pins and small end bearings just to eliminate that one as well. They are fairly cheap.

I hope there aren't any errors in this post as I have lost the ability to edit and even though I do preview my posts I don't always get it right.
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[color=#808080][size=9]Yes,.. I too know how to waste Time and Money,...