I noticed that you were looking to adjust Prestige to be more accurate. I found this article on Bleacher Report that lists all Division 1 schools by prestige based on a number of factors, and I have found it to be very accurate in my opinion.
http://bleacherreport.com/articles/2724317-how-much-does-your-college-football-team-matter#slide0
How I have used it is I place all schools ranked as follows by the corresponding prestige in game.
110-130: 25 Prestige
100-109: 30 Prestige
90-99: 35 Prestige
80-89: 40 Prestige
70-79: 45 Prestige
60-69: 50 Prestige
50-59: 55 Prestige
40-49: 60 Prestige
30-39: 65 Prestige
20-29: 70 Prestige
6-19: 75 Prestige
1-5: 80 Prestige
Only issues with this article is that it has Idaho and not Liberty, they can probably just be swapped. Also, FIU and FAU are both rated at 25, you mentioned placing prestige on coming results, I think that places too much emphasis on a current head coach. I think those 2 schools are find where they are, but you may disagree. There are a few other schools that get shafted a little bit, like Air Force and Navy who are now generally bowl teams every year. But again, it can be argued that is due to current head coach more than the teams prestige.
Anyways, this is how I always set up my new leagues, but I don't know how to program it in, so I make the adjustments before every game.