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In QGIS, I have multiple layers that are not lining up, despite the fact that I have enabled "on the fly" projection and clicked "Save As" to reproject specific layers to CRS EPSG: 26915 (NAD83/UTM zone 15N). I've also tried "Define Current Projection" from "Geometry Tools." No matter what I do, I can't seem to get layers to line up. The oddest part about it is that about half of my shapefiles line up in one part of the map, and the other half line up in a completely different part. All of the previous questions I have found on this topic have not helped me solve this issue, or I'm too dense to understand.
The layers I'm working with are a variety (polygon, point and line), as well as .shp and .kml.