Hey there.

Just convert your model back to polys, then make sure that all of your vertices have a partner. Poly combine all the parts, merge the vertices then convert the whole thing back to sub-d's.

Its best to do all of your merging verts, poly splitting, etc, in poly mode, then just convert to sub-d's at the end for final detailing. Thats what I do anyway. I just keep two shortcut icons on my shelf, one for converting to polys, one for converting to sub-d's, so I can quickly change my model between them to see how its looking.

Hope this helps, your model looks like its coming along well!