Sorry but now you lost me :
QUOTE
Furthermore I have to combine the meshes
Yes, otherwise how are you planning to have vertices shared between two separate meshes ?
QUOTE
But after merging multiple edges, I can reduce the number of vertices with mergevertices all the same.
That shouldn't be the case as merging edges does merge the vertices ...
QUOTE
I can see, which Vertices aren't connected with edges and I can take them out
Vertices are always connected to edges, they don't exist individually !
Are you sure you model is correct and doesn't have faces duplicated on top of itselves ?
Try to run the "polygons cleanup" as what you described doesn't make any sense ...
Or maybe I misunderstood what you're describing.
Guyb.