Two outs. This out of the BR (batter-runner) broke the sequence of runners so there is no chance for a subsequent "force out."
Three outs. This out on R1 (runner who started at 1B) is a "time" play (actually an appeal by the defense that R1 failed to re-touch 1B after the BR's fly ball was first touched) and, because it's the third out of that half-inning, no run may score after the "time" that it occurred.
Yes, because R3 (runner who started at 3B) touched home plate BEFORE the precise time that the defense successfully appealed R1 failed to re-touch 1B.
