There are several drop off parking areas along the trail so you can run it in sections. The Falcon Guide guide "Hiking Indiana" has good information on seven trail segments and parking areas at each end of the segments along with good information about each segment.
The Knobstone Trail (KT) is Indiana's longest footpath. It is stated to be a 60-mile running trail but most of the maps for thru-hikes that I have seen list it closer to 45 miles. It goes through several state forests and state parks. The trail starts at Deam Lake State Recreation Area.
You can find more information about the trail on the Indiana DNR website