R1 on 3B R2 on 1B

[DonP]

Situation for discussion
R1 on 3B, R2 on 1B 1 Out. B3 hits a deep fly to Center. R1 waits on 3B for catch, runs home. R2 thinking there is 2 outs, runs past second before he realizes there is only one out, while retreating to first, he misses second base. The ball is thrown to first base for the tag up put out. The defense also appeals the missed base at second.
Q1 Does the run score? Rule book reference for \ against
Q2 Is the second base retreat retouch miss a defense appeal or can the umpire automatically call him out?

I am interested in hearing your arguements for and against. My partner and I had different perspectives on the proper rules and administration.