Your version of resume ranking is somewhat simplistic, because you simply rank the wins and compare them all head-to-head for quality. Furthermore, you do not seem to be taking anything into account other than the score (Boise State dominated Oregon, and the score differential would have been much bigger if not for a few sloppy mistakes and running the ball a lot once it was clear that time was a factor at the beginning of the fourth quarter) yet you only give Boise a medium edge in the head-to-head result).
I would compare each team's wins against similar opponents, using the following statification system: games v. top 10, games v. 10-25, games v. 25-50, games v. 50-100, games v. 100+. This makes sense because an elite team should never, under any circumstance, be losing to a team above #50 and should sleepwalking against FCS schools and teams that might lose to FCS schools. Furthermore, I would give a increased weight to the head-to-head, because there is no head-to-head tree that puts Oregon over Boise.
Top 10 (weight = 8)
Oregon: (USC, blowout; Boise State, non-competitive loss)
Boise State: (Oregon, non-competitive win)
Edge: Boise State (medium, +2)
10-25 (weight = 4)
Oregon: (Cal, blowout; Utah, competitive win)
Boise State: None
Edge: Oregon (extra huge, +5)
25-50 (weight = 2)
Oregon: (Washington, blowout; UCLA, non-competitive win)
Boise State (Fresno, blowout)
50-100 (weight = 1)
Not going to bother listing every game, it's an obvious draw.
100+ (weight = 0.5)
Edge: Oregon (slight, +1)
Edge: Boise State (big, +3)
Oregon: 5*4 + 1*0.5 = 20.5
Boise State: 2*8 + 3*4 = 28