So I just recalc'ed the QB ratings and resorted the list after taking out each teams YAC from the QB's calculation. It's not perfect, as some QBs' didn't play the whole season, and I'm taking out a whole season of YAC from their yardage (see Vince Young), but suprisingly the order of the list didn't change that much.
Code:
W/O YAC W/ YAC Player
1 2 Brett Favre
2 1 Drew Brees
3 4 Aaron Rodgers
4 3 Philip Rivers
5 5 Ben Roethlisberger
6 6 Peyton Manning
7 7 Matt Schaub
8 8 Tony Romo
9 9 Tom Brady
10 10 Kurt Warner
11 11 Eli Manning
12 12 Donovan McNabb
13 16 Carson Palmer
14 13 Joe Flacco
15 14 Kyle "Pro Bowl" Orton
16 17 David Garrard
17 15 Jason Campbell
18 20 Matt Ryan
19 19 Alex Smith
20 21 Jay Cutler
21 22 Chad Henne
22 18 Vince Young
23 23 Matt Hasselbeck
24 25 Matt Cassel
25 27 Brady Quinn
26 28 Mark Sanchez
27 26 Ryan Fitzpatrick
28 30 Josh Freeman
29 24 Marc Bulger
30 31 Jake Delhomme
31 29 Matthew Stafford
32 32 JaMarcus Russell