i thought you had different materials on each side of the head... this isn't true?

how did you duplicate?
duplicate special with a negative scale and then freeze transformations?
if so then reverse the normals.
in the panel menu check Lighting > Two sided lighting to off
that way the back of faces will show up black and it will be easier to tell when your normals aren't agreeing with each other.
if your inital merge fails and you have a distinct line than can't be resolved by soften edge then something went wrong

how i do a 'mirror merge' is to...
not use mirror geometry because whenever i used it, it would sometimes do funny things... (although that was when i first started so i might have had some settings wrong)
duplicate special with a negative scale (or just duplicate and then give it a negative scale)
combine the pieces (i just hit the shelf icon but i think its in mesh > combine)
select a whole lot of verts,
merge vertices with a very low tolerance
if needed then grab the edge loop that was in the middle and soften edge