Well, I am pretty confident almost all the schools in Michigan will look at you if you have retaken classes. But you might get a little 'ding' for it. I retook 2 classes before I even became fully committed to PT school...and then had to retake 3 more to even apply...I got accepted to UM-Flint and Andrews University.
I was told by UM - Flint, Andrews University, Grand Valley and CMU that they take your highest grade achieved..after 2 classes, you may get 'dinged' a little but you better make sure your retakes are 4.0s. In terms of Michigan schools, UM - Flint and Andrews University would be your best choice in terms of getting accepted...(however, Andrews is a private school and costs $90,000 for in-state tuition alone...probably why its kinda easy to get into for only having 32 seats..lol). Grand Valley and CMU are just really hard schools to get into...they focus more on grades that anything else.
UM - Flint focuses more on your experiences and what you have achieved more recently in terms of grades, exams, etc...So IF your interested in the Michigan area, UM - Flint would be your best option IMO.