I'm using Hooch's fixed version of Cannonfodder's MDLDecompiler, I upgraded to that after getting tired of using Notepad++ almost all the time before decompiling anything.
Use the Version 0.4 of Cannonfodder's MDLDecompliter
As for the .VTX files, it isn't missing any of the ones you mentioned. However, it still fails to grab the model itself. I'm not too sure what the issue is.
*sniff* *sniff* I smell bullshit

I never seen Source 2010(L4D2) - 2011 (Portal 2, Alien Swarm) models with sw.vtx or dx80.vtx. Most of the time dx90.vtx is missing too.