American Legion "Time Called"

[first2third]

First off, I am calling my fault on this one. I know I called time too early. However let's suppose I didn't mess up.
Sit: Bases Loaded no outs. Infield pulled in bottom of the seventh tie game. A shot to the shortstop that skips into his glove. My awesome partner has a great angle and yells no catch and gives a safe signal on the catch. The shortstop throws home. R3 slides home in a cloud of dust, I yell force and mark the out. The catcher looks to throw to first, realizes that the play would be to risky and holds on to the ball. Catcher pauses throws the ball to the pitcher who then walks back to the mound area. He is on th dirt (not that it matters). I call time and go to sweep the plate. Well there is no runner on second the second baseman notices and yells at the pitcher to throw it there. He does and my partner yells force and marks the second out (apparently R1 fell and twisted his ankle and limped off the field toward the first base dugout as the play initially took place). When the pitcher throws to second for the second out, R2 who is now on third breaks for the plate. I am done sweeping the plate at this time and the batter is in the batters box. The batter moves into the diamond as the catcher contact him to get into position for the throw home and just avoids the throw because it is up the line a little. The catcher catches it and reaches back to tag the runner but doesn't make it. Needless to say, The defensive coach wants interference on the batter and a third out. The offensive coach wants the run to count.

1) Here is what we did. Called the runner out at second and then sent the winning run back to third, due to time being called. Really no one said much both coaches were great about it. Was this the right thing to do?

2) What if I hadn't called time. I believe that I do have to call the runner out at the plate for interference. Right?