Subjunctive/indicative

If she was not in Paris, then it made sense it was not her that picked up the phone when I called her home.
-"... it made sense that it was not..."

If Bill was the governor of Kansas, then he had been the president from 1992 to 2000.
-"... then he was the president..."

I wondered if she were here.
-It should be 'was' instead of 'were.'

I asked if her sister was here.
-Okay.

    They sound equal to me.

    No, they don't.  The circumstance must have confused me.  Thanks, GG.

I understand. It's common to say "That was her!" or "That was not her!" even though by the laws of grammar it should be the nominative "That was she."  Often our ears protest hearing "It was she," thinking it sounds absurdly pendantic, stuffy, or old fashioned. But once you have the rest of the phase included: "she who answered the phone" then it becomes clear that the nominative is necessary.