A number of years ago when I was looking at colleges, I was in a similar situation. Slightly higher ACT score, but slower on the running side. I primarily decided between Macalester, St. Olaf, and La Crosse. I toured at St. Thomas and talked to some friends who go there, but I really wasn't fond of the atmosphere (commuter college-everybody leaves on the weekend, more of a state school party atmosphere and felt fake in my opinion). La Crosse and St. Olaf both seemed to have strong team atmospheres, and I liked Coach Lundin quite a bit. Coach Stanley wasn't at La Crosse at the time, but I have heard good things since then. It appears that both of these teams will compete at the national level in the coming years, with La Crosse having more sprinters and therefore a better track program. Macalester is definitely a better academic school than La Crosse or St. Olaf, and has the advantage of proximity to the Twin Cities and the career connections that can be made there. That being said, the XC and track teams leave something to be desired... They have a new indoor track that is quite nice though, and I always enjoyed racing on their outdoor track in high school.
As for religious affiliation, St. Thomas is fairly Catholic, but it is a larger school so there is more diversity (and lots of churches in the area to choose from). St. Olaf is associated with the Lutheran Church, but I asked around and they have a tight Catholic student group on campus, along with a Catholic church (St. Dominic's) within walking distance. Macalester and La Crosse are both unaffiliated.
Outside of those four schools, I can't offer much insight as I didn't tour/do overnights anywhere else in the area. I encourage you to contact the coaches to see about visiting the team and getting a feel for team atmosphere and academics. If you narrow your Midwest schools down a little, you could think about an overnight visit to see if that seals the deal.
Best of luck!