last i used that mirror geometry it combined the two pieces of geometry if you haven't checked it to merge
if you checked it to merge then you wouldn't need to do the merge vertices

if your model is symmetric then you can align all the verts in the middle of the model so that they are all straight and move the pivot point inline with them (hit insert to move pivot, or home on mac(?)),
then use mirror gometry with merge meshes checked on(i prefer duplicate special, because it doesn't screw up as much)

if you did do the duplicate special way then mesh > combine them, and then you can select all the verts, go to merge vertices > option box and change the threashold to something like 0.001, since the verts should all be on top of each other they will merge without problem