[UmpTTS43]

I think kopan99 said it best and laid it out logically. This is the closest thing I have been able to find in my library concerning this sitch.

Taken from The Wendelstedt Umpire School Manual Pg. 115 Appeals, Copyright 2008

"P22: R2, R3, two outs, 1-1 count. The batter hits a ball down the right field line. As he reaches the 45' line, the BR severely twists his ankle and falls down. R3 easily scores, and R2 touches third base and attempts to advance to the plate. The right fielder, not seeing the BR lying between home and first base, throws the ball to home plate. The throw beats R2 easily, and he is called 'out' by the plate umpire. The defense, then seeing that the BR has not yet reached first base, tags first base, appealing that he never touched it.
Ruling: The umpire should not recognize this appeal. A runner cannot be appealed for 'never reaching a base'; only for not touching one on his way past it, or for not legally tagging up from it. In this situation, the third out has already been made at the plate on R2. R3's run counts. The defense is required to know that the BR has not reached first base, and if they would have retired him at first base, instead of throwing the ball to the plate to retire R2, no runs would have scored."

With kopan99's rule cites and Wendelstedt's interp, I now know how I would rule on this.