Pulled foot mechanic and timing

[PatF]

Sorry in advance for the length of this post.

Tournament game. Managers are told by the tournament director that they are the only reps from their teams allowed to address the umpires. They are also told if they have a question on a call, they are to request time and go the umpire that made the call.

2 outs, runner on 2B. I'm BU in position C. Grounder to short stop. Throw to 1B clearly beats the BR, but I am straight-lined on the throw. I signal the out and am unaware that the throw pulled F3 off the bag. BR heads for the dugout and defense heads off the field. There was no immediate reaction or response from the team at bat that would indicate a pulled foot.

First base coach goes to my partner at the plate and says that F3 was off the bag. Partner tells the base coach that only the manager can appeal the call and that manager must go to the umpire that made the call. Manager is in the dugout and apparently didn't even see the play. Base coach relays this info to manager. Manager comes to me and appeals the pulled foot. I go to partner and partner verifies that F3 was off the bag. Defense has totally cleared the field and team at bat has begun to take the field by this time.

How should this situation have been handled and what should have been the final ruling?