Tag Up Appeal: Run Scores?

 
With 1 out and runners on 3rd base (R3) and 1st base (R1), R1 is running on the pitch. The batter pops out to right field (for the 2nd out of the inning), while R3 properly tags up at 3rd base and scores. The defense realizes that R1 did not properly tag up, so as R1 is returning to 1st base, the defense throws to 1st base to retire R1 for an inning-ending double play. R3 scored well before R1 was retired at 1st base. Was the inning-ending out (as R1 returned to 1st base) a timing play or a force play? Does R3's run count?
 
Call
It may appear that R1 was "forced" to return 1st base. If the inning ends on a force out, then no runs score. Actually, R1 was not forced from 1st base (B1's fly-out removed the force) and R1 is not forced to return to 1st base. Since this is a timing play and R3 scored before R1 was retired, then R3's run counts.

Extra Credit Question:
Similar to above... 1 out, R3 on 3rd base and R1 on 1st base, BUT both R3 and R1 are running on the pitch. The batter flies out for the 2nd out and then R1 is doubled-up  at 1st base to end the inning -- but since R3 was running on the pitch, he did not properly tag up. R3 tagged home before the pop-up was caught in right field  and R3 was in the dugout before the inning-ending double play was completed at 1st base. Does R3's run count since he never properly tagged up at 3rd?
 
Call
The answer is similar to the above -- this is a timing play, so since R3 scored before the final out of the inning, then R3's run counts. The fact that R3 did not properly tag up does not matter -- UNLESS the defense properly appeals the issue. On an inning-ending play, the defense can appeal up to the time that all the infielders have left fair territory. If the defense properly appeals, this would be the 4th out, and the run would not count.