As a Duck, I'd say Stanford definitely "handled" Oregon's running game in that 17-14 overtime loss. And perhaps that's why Oregon has apparently improved it's kicker (missed OT field goal attempt) and rumor has it opened up more passing in the offense (putting pressure on defense to not cheat to defend the run so much).
We don't know if those two parts of the Oregon game have been successfully fixed yet, but it appears the Oregon staff is working on them.
I hope you are right, I really do. The more you guys tweak and change a system that Kelly had clicking along, the better our chances are especially early in the season.