One option I wanted to add just for total accuracy in score keeping (and the issue did come up in a recent game), when the option window comes up after a third strike, the only two options for safe are passed ball third strike and wild pitch third strike. If the option for reach on error or fielder'...

The correct way to score it is to give the base via an error on the position that obstructed (E4). Rule 10.12(b) states "When an umpire awards the batter or any runner or runners one or more bases because of interference or obstruction, the official scorer shall charge the fielder who committed the ...

It is definitely an error, regardless of what happens next, and you enter it by recording the Foul ball and then doing Misc->Assign Error

There is definitely only one error on this play, because only one runner advanced. If you charge an error, that means that it is an error regardless of what happens next. But if he had nailed the runner at second, you wouldn't have given him the first error, so it is very clearly wrong right there.

Just a quick note here, you mentioned it was a bad hop, which would mean it was a hit--although I am only going by what you said.