[Rufus]

Bases loaded, 2 outs. Grounder hit to F4 who, because he's 5, tags R1 rather than throw to 2nd or 1st for the force. Before he tags R1, however, R3 crosses the plate.

Based on 4.09(a) I think the run counts because R1 was retired via tag instead of a force. Is that correct?

4.09 HOW A TEAM SCORES.
(a) One run shall be scored each time a runner legally advances to and touches first, second, third and home base before three men are put out to end the inning.
EXCEPTION: A run is not scored if the runner advances to home base during a play in which the third out is made (1) by the batter-runner before he touches first base; (2) by any runner being forced out; or (3) by a preceding runner who is declared out because he failed to touch one of the bases.

BTW, I'm enjoying having these rules discussions with my 16YO who's in his second year of umpiring. Great fun to dissect and discuss a game that he's no longer playing but still loves.