I think you probably put Illinois in because their losses would (presumably) be to Penn St. and Oregon (and the alternative, where beat Oregon and lose to someone else, is probably even better), and the overall schedule looks tougher.
I think the impact of those "top-25" victories will be a lot smaller than you imagine. Yes, Nebraska was a top 25 team early in the season at the time we beat them. But Indiana also played Nebraska, and beat them far more handily than we did. Kansas is clearly not the team preseason voters thought they were. If Indiana loses to Michigan (as in your scenario), obviously that helps us. If Indiana thrashes them (and I dunno, their other loss is a close one to Washington or MSU), that could be another team that we beat, but Indiana beat "better."
A lot of it would also probably depend on how Indiana loses its two games (and how we lose our 2nd). If they get drubbed, it would hurt them in the advanced metrics, which would help us. If they keep it close, the way they've been blowing opponents out will continue to give them an edge in the advanced stats.