Press Pins and Balance

[modok]

total MINUS small end =big end

OR
total MINUS big end =small end

(or in your case small end and piston)

Perfectly fine to do so either way
If you get different results one way VS another go with whatever you think is more accurate.

The only reason I ever check the small ends and big ends is to make sure they DO total the total. Just a check to make sure my fixture and procedure is working correct. If my small end+big end comes up one or two grams short of the total I know I need to adjust what angle I'm hanging the rod or level the scale, or ect. Just a double check.

And I also like to stack a lot of things on the scale at once, but that is just to reduce tolerance stack. Adding each part separately will add up to the same if your values are correct.
Simplifying it like that is handy also to reduce complexity, for instance your bob weight could be... (for a 90degree vee)

Total of the rod and piston(including rings, pin, clips,ect),+one rod big end, + all four bearing shells.
DONE, Simple isn't it

[modok]

Paper towel thing seems wrong.
The piston should not be exerting any torque about the pin. it should be supported so it no twisting moment is transferred to the rod.
I would THINK....
To measure big end... The piston should be hung by two strings so it cannot twist or flop, so the small end of the rod is supported by the pin only, and big end supported at it's the center and that goes down to the scale.

To measure the small end+piston, set the piston on a leveled scale and hang the big end from it's exact center.