For geom switching, I don't really see why you'd have to get the .obj into an editor, unless that editor is a 3D modeler.  As long as the connecting points to the pelvis and r/l thighs are exact, it is going to look seamless.  Even if the points don't line up, it's not going to explode.  There will just be visible holes, especially when things get bent.

If the morphs aren't re-worked for that area, it's just not going to have any effect.  The only time there's an explosion is when the polycount is the same but the vertice order is off and those polygons have no clear direction in which to move from one shape to another.  There could be other reasons, I suppose, but that's what I'd put my money on.

.