Here is a link about the 1904 NC:
http://tiptop25.com/champ1904.html
Minnesota 1904
I covered Minnesota in my 1903 article. They lost their best players from that team, tackle Fred Schacht and end Ed Rogers, but rolled right along, finishing 13-0 and outscoring their opponents 725-12, which got them a lot of national attention. That was-- and still is-- the second most points ever scored by a major (FBS) college football team in a season. Harvard 1886 holds the record of 765 points. As a result of the publicity, Minnesota might have edged out Michigan for a higher ranking if there had been an AP poll (Caspar Whitney ranked them higher, as covered below). However, Minnesota played 3 more games than Michigan did, and the fact is that on a per game basis, Michigan outscored Minnesota 56.7 to 55.8.
Minnesota's schedule wasn't much better than Michigan's. They did play 5 major teams, compared to 2 for Michigan, but only 2 of their opponents would have likely finished in a top 25, the same as for Michigan. And none of their opponents were as strong as Chicago. Minnesota's top two wins were 28-0 over 5-3 Wisconsin (the same score Michigan beat them by) and 17-0 at 8-2 Northwestern (who lost to Chicago 32-0). They were rather unimpressive in an 11-0 win at 7-4 Iowa, and even more unimpressive in a come-from-behind 16-12 home win over 9-3 Nebraska, who, as mentioned above, was not as good as they had been the previous two years. Had there been a top 25, Nebraska would have likely finished just outside of it, around #30.
It's that Nebraska game, and to a lesser degree the Iowa game, that separates Michigan from Minnesota. Michigan was not threatened by any opponent. And Michigan victim Chicago was a much tougher team than anyone Minnesota played (Chicago beat Wisconsin as well as Northwestern). So unlike 1901, when nothing really separated Michigan and Wisconsin, and 1903, when the same could be said for Michigan and Minnesota, in 1904 you can select Michigan over Minnesota for Minnesota's one bad game against Nebraska and Michigan's one big win over Chicago.
On the other hand, Minnesota was Nebraska's biggest rival, the team they most wanted to beat every year (while Wisconsin was Minnesota's biggest rival). And though Nebraska was not great, they were very good (they were 9-3, and beat Illinois, who tied Chicago). And Nebraska was the only team that came within a touchdown of Minnesota, and in fact they were the only team that scored against Minnesota. So it was clearly just one bad game, and thus there is plenty of reason to believe that Minnesota was about equal to Michigan.
But back on the first hand, one bad game is more than Michigan had. So I'm boiling this national championship analysis down to Michigan vs. Penn.