It's fixed, I got my normal tones back. For the sake of trouble shooting I started a new profile before uninstalling and started initial setup, the tone was still broken up until I got to the noise calibration setup. That's when everything returned to normal, I backed out and loaded my main profile and it seems all good to go. I don't switch guitars often and rarely use the re-calibrate setting, so I didn't even think of trying that.
I'm not sure if it was the cdlc that I played, but this has not happened to me post remastered edition. It was the first time I played or put it into my folder (Agent Orange - Bloodstains) couldn't find it on the list of "dead tones and misc problems" thread. In any case if this happens again I believe you can fix it by simply re-calibrating your guitar.
Thanks for the help with the troubleshooting guys.