mirror geometry is a broken function that seems to only work on simple meshes.

you should make sure the verts on the border edges are aligned the way you want them to be then move the pivot poin and snap that to one of the verts (push the insert key and hold down x to snap to grid or v to verts)

then find duplicate special (i think its in edit) and go to the option box. reset the controls and set the x axis (or whatever axis you're mirroring on) to -1

hit duplicate and then merge the two meshes

then select the border edges (can do this by right clicking while holding down shift or doing it from the menus select > border edge) and get all the border edges you want to merge

then hold down ctrl and right click to bring up the markingi menu. go to To verticies > contained vertices (or which ever option gives you all the verts on the border edges and then merge the verticies (make sure your merge thrteasehold is low or they will all merge to one point)



in short all you do is duplicate the geometry and merge the vertices