All good comments!

Shp4Man - Thanks. The Edge derailleur sounds like it may be as good, if not better than the Cyclone.
Treebound - Funny you should mention the chain stretch. Just after this last riding season, I measured and it's spot on. No issues should be there. I do think you make a good point about the setup being a 6 speed and after reading about the Command shifters, it sounds like they are for 7 speeds. But, I suppose that's ok. I say that because it ties in with CV-6's comment. It has indexed properly before. I rode it for over 2 years without a hiccup, then the issues started.
I'm not sure if any of this helps or just helps cloud the problem issue(s).

Thanks for the comments. Keep 'em coming!