Spizzlepop,
I believe the scoring would be to award put outs to the fielder closest to each out. Probably all the short stop, who was most likely closest to R1 running past R2, the pop up itself and R2 when it hit him. Not having seen the play, I can't say if the second baseman wasn't involved in some way.
The notation I would use is 666-TP, 'cause there is no other way to describe something evil like this. I'd probably put a few stars around it and add some notes so if I ever flipped through that book again (years later) so I could tell the story accurately.
Probably the only case I've ever run across where a batted ball hits a runner and the hitter doesn't get credit for a hit.
Bizare play on many levels...