The .blend file you provided does not have the same geometry, but this should be adaptable. Select the middle edges/vertices as shown in the picture. In the .blend you provided, this is as simple as alt clicking on an edge. In your real model, it may involve a bit more finagling to get the selection where you want. You can select multiple edges/verts by holding shift and clicking, or holding ctrl to get the shortest distance between two points. You could also use the circle, box, or lasso select for this. Anyways,
delete them x > delete vertices
select a region of edges/vertices and press 'F' to fill in a face. This may be more or less difficult depending on how symetrical the front/back topology of the model is. Its the least painful when there are the same number of edges.
Not sure why those images got out of order, or how to fix them. Sorry about that.
Fill in the rest of the faces, if you need more resolution in the middle areas, use the ring tool, 'ctrl+R', or knife tool 'K' You can peel back the sides with proportional editing 'O' turned on, make sure to hide the other leg, or turn on connected only, so you don't drag it along. You could also switch to sculpt mode and use the smooth tool.
This image uses sculpt mode smooth.
This is the same process but without deleting the vertices ALL way up.
There's no one way to do things in modeling, this is your little world and you can do it however you like. That said, it would be much more efficient to make your legs split from the start, than to make them one block and split them later.