If you think of "the width of the A pin" as one subject and "the width of the B pin" as another subject then you can replace them with simply "the A pin" and "the B pin" and see what seems right.
a) The A pin and the B pin are different.
b) The A pin and the B pin is different.
You can see that a) is correct.
I'd suggest however that "The A pin and B pin have different widths" is a more natural alternative.
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