Batter missed base on late throw to first
 

B1 grounds to F5. F5 throws "late" to F3 who is touching first base with his foot. B1 "beats" the throw to first. He overruns first base but fails to touch the bag. Is B1 out at this point (simple force), or does F3 need to take any additional action to "appeal" the missed base?

A missed base requires an appeal. ANY missed base.

And it isn't a force. Only runners that were on base already can be forced. it just sorta looks like one.

Since the "play" was already made on the bag, should F3 just tell the umpire "He missed the bag!"? Or does he need to make another "play"?

Also if there were two outs, and a runner on third should score, is the appeal a "timed" play?

He can claim the missed base and touch it, or tag the runner. It has to happen before the runner returns to the base. Otherwise the miss was corrected.

If the appeal is upheld the run would not score as the batter-runner was therefore out before touching first base.