First mirror the model like usual with mirror geometry.
Then go to the front view and select all vertices that makes that ugly line(the "border" vertices that you want to become normal vertices)
Then go to the Polygon menu >> Edit mesh >> Merge, hit the "box" to the right of it to open the options.
Here change the threshold to a really small amount(If you have the vertices on a exact straight line, the higher the threshold the larger is the risk that you merge som vertices that you dont want to merge.
If you want the vertices to be on the exact same line use this Mel command.
"move -a -ws -x 0;" But replace x with Y or Z if needed, and change the zero to how far away from the center it is, or more simply just move the line to the center so that it aligns without having to use any measuring tool.
I hope it helped.
Edit: Remember if you duplicate your model then you have to the Polygon menu>>Mesh>>Combine before you can select and merge your vertices.
Why does merging vertices take long time for you? It is like 2-3 cliks and then its done, or did you try to merge them one at a time?