Try to export the layers as separate files, then place and expand them in AI. After the expand, each object will become a group which you can color. Use symbols and object styles for consistent appearance. I'm not aware of any script or function to parametrically organize imported layers with intact references.
You can use your first file as a template to make a file with Layers in the order and name you want. Make sure that Paste Remembers Layers is checked in the Layer flyout menu. Then just copy the original file. Paste into a new file, select all and delete. Then copy and paste from the second and ensuing files into each new file on the appropriate layer. They'll probably come in on Layer 1. Drag the colored square at the right of the layer (making sure it is a large square) to the layer you want.