What did you do with the O2 sensors?
Sorry I have been so delinquent in responding. The Stock head pipes from my FLTRSE3 were replaced with a set from my buddies 09 FLTR. I simply unscrewed the sensors from the 110" pipes and screwed them into the 96" pipes. My friend had them laying around (he went to a D&D fatcat) so I swapped him a 2008 HD touring cover I had leftover from my 08 RG. The head pipes and heat shields from a 96" seem to be identical except there is no Cat hiding out in there.
I purchased my bike (Spooky) on Halloween day and rode it home 32 miles. Pulled the heat shields off, and the rear cyl pipe was already yellow as was the area where the Cat lives. Installed the 96" pipes and replaced the baffles with Fullsac 2.25". I think I am going to install the TTS and a set of Andrews cams (follow Fullsac's knowledge) in the spring when I pull it out of the basement and can fire it up.
Now I have a 110" header pipe with the cat still in there, full set of heat shields, cross over pipe and mufflers from a 09 FLTR; Gonna list them on E-Bay. If you watch E-Bay you can find the 96" head pipes for sale or as fellow CVO owners have suggested ask your dealer if he has one. I would think If you can get it for <$100 you did OK.