Apologies, misremembered the context of this post.
In your case, it is neither weights nor uv_1. It's the shape of the mesh. I don't know how this works or how to explain it the right way, but if the mesh is meant to be affected by the morphs of the right side of the body, it must be on the right side of the body only, same with the left.
- in edit mode disable Limit selection to visible. Holding Ctrl, select one side of the pants, press Ctrl L, choose UVs to select the whole side;
- press P - Selection to separate, rename the separated side to pants_l, the other one to pants_r;
- repeat both steps on the reference, naming them as ref_l and ref_r;
- select pants_l. See the blue line? See how a little bit of the mesh crosses it? You need to press B, select that area of the mesh that crosses it ( not in the crotch area, just when the legs start to part), enable Proportional editing, press G X, scroll the mouse wheel up until the radius is appropriate, and move the mouse. The goal is for the mesh to not cross the line. You don't need to do it at once, when the upper portion of the mesh is good, you can deselect it;

- once done, select pants_r and do the same thing;
- now you just transfer weights and uv_1 from ref_r to pants_r, then from ref_l to pants_l, then you join them into one and remove doubles;