Okay, so it can no longer be avoided: when the final model run takes place one week from today, the S-Factor is going to end up showing Duke as a number one-seed. Either Connecticut or Stanford, almost unanimously shown as one seeds by other bracketology sites, is going to be shown as a two-seed. Connecticut will be no lower than #4 overall if they win the Big East tournament, but if they lose in the championship game or before, they will almost certainly be shown where they are right now, in the #5 overall spot.
I outlined the case for Duke back in February. Since then, two bracket-changing events have happened: Duke lost to 50th-ranked-in-RPI Miami, and Duke killed it in the ACC tournament, triumphing in the championship by 19 points over North Carolina. On the one hand, that loss to Miami is the only loss by any of the top 5 teams (Baylor, Stanford, Notre Dame, Connecticut, Duke) to a team outside the top 25. On the other hand, Duke won both the regular season and the conference tournament of the ACC, and they went 5-0 against top 25 teams since Chelsea Gray's injury.
Still, Connecticut and Stanford seem like objectively better teams. They have losses only to teams that will be #1 or #2 seeds in the tournament, and they both have more blowouts of 20+ points (Connecticut 24, Stanford 18, Duke 16, none since Chelsea Gray's injury). Connecticut at the very least should definitely be ahead of Duke, if for no other reason than the 30 point blowout they handed to Duke.
Florida Gulf Coast
Conferences with multiple bids:
Big East: 8
Big Ten: 6
Big 12: 5
Pac 12: 4
Atlantic 10: 4
Missouri Valley: 2