[greymule]

So the R1 run would count, even though they were touch out order. Would that be considered as a R2 passing R1?

No, if a runner misses a base and then a following runner touches that base, the following runner is not considered to have "passed" the preceding runner. Passing means physically passing.

The appeal on a runner who has left before the first touch that leads to a catch is never a force play. If it's the third out, any preceding runners that scored before the out count. Following runners who scored do not count.

An appeal of a missed base can be either a force play or a time play, depending on the circumstances. But know that the various codes are not completely aligned on this matter. For example, an appeal of a missed base might be a force play in baseball but not in softball, even on the exact same type of play.