Easiest thing to do to delete a layer is to select the components that are on that layer already and then right click and remove objects from that layer, then you should be able to delete it just fine.

One of the biggest tricks I have learned with layers is that you have to first select in Object mode the pieces of your model that you want on a single layer and then using the add layer with selected objects should do what you are looking for. Maya sometimes runs into problems with not removing items from a layer if that object was created or duplicated from an object on another layer. As for wireframe colors make sure you have show wireframes on shaded on. Selected objects will default to the selected objects wireframe color despite the layer color.

I have attached a pic to see if this is what your are looking for.