[OCcardinal]

We beat a 1- and a 2-seed at home, lost to two 4-seeds away, and tied an 8-seed and an unseeded tourney team away. The Cal tie might have made a difference, but impossible to know.

Compare Stanford's record against a couple of the two seeds:
Penn State: 
Tournament Team Results
Lost to: a 3 seed (Stanford) away, a 4 seed (Michigan State) at home, and a 6 seed (Ohio State) away 
Tied: 5 seed (Georgetown) at home
Beat: a 4 seed (Michigan State) at a neutral site  
Didn't play Northwestern
Nontournament Team Losses and Ties
Lost to: Nebraska away
Tied: Iowa away and Indiana away

St. Louis: 
Tournament Team Results
Lost to: a 1 seed (Notre Dame) at home 
Beat: a 3 seed (Arkansas) at home 
Nontournament Team Losses and Ties
None (same as Stanford)

In addition to what you mention above, Stanford has an away win over unseeded Arizona State.  So it's 3-2-2 against tournament teams (including wins vs a #1 and #2) compared to Penn State's 1-3-1 (1 win vs a #4) and St. Louis' 1-1 (1 win vs a #3).

You are right we can't know how much the Cal tie hurt, but that was our only moderately adverse result against any team that was so much as unseeded. With the tie we dropped from #9 in the RPI to #11 (from 1 spot behind St. Louis to 3 spots behind) and I'm assuming that the larger gap was too much for the committee to overcome using judgment. In fact, with RPI #5 North Carolina as the #2 seed in our group, I don't think the committee moved us up at all.  RPI #9 Arkansas got St. Louis as the #2 seed in their group and RPI #10 Virginia got Penn State as their #2. So it looks like Stanford is at least the 3rd lowest #3.

[OCcardinal]

We beat a 1- and a 2-seed at home, lost to two 4-seeds away, and tied an 8-seed and an unseeded tourney team away. The Cal tie might have made a difference, but impossible to know.

Compare Stanford's record against a couple of the two seeds:
Penn State: 
Tournament Team Results
Lost to: a 3 seed (Stanford) away, a 4 seed (Michigan State) at home, and a 6 seed (Ohio State) away 
Tied: 5 seed (Georgetown) at home
Beat: a 4 seed (Michigan State) at a neutral site  
Didn't play Northwestern
Nontournament Team Losses and Ties
Lost to: Nebraska away
Tied: Iowa away and Indiana away

St. Louis: 
Tournament Team Results
Lost to: a 1 seed (Notre Dame) at home 
Beat: a 3 seed (Arkansas) at home 
Nontournament Team Losses and Ties
None (same as Stanford)

In addition to what you mention above, Stanford has an away win over unseeded Arizona State.  So it's 3-2-2 against tournament teams (including wins vs a #1 and #2) compared to Penn State's 1-3-1 (1 win vs a #4) and St. Louis' 1-1 (1 win vs a #3).

You are right we can't know how much the Cal tie hurt, but that was our only moderately adverse result against any team that was so much as unseeded. With the tie we dropped from #9 in the RPI to #11 (from 1 spot behind St. Louis to 3 spots behind) and I'm assuming that the larger gap was too much for the committee to overcome using judgment. In fact, with RPI #5 North Carolina as the #2 seed in our group, I don't think the committee moved us up at all.  RPI #9 Arkansas got St. Louis as the #2 seed in their group and RPI #10 Virginia got Penn State as their #2. So it looks like Stanford is at least the 3rd lowest #3.