After the previous failures I had with installing CyanogenMod, I conversed some colleagues who have the same phone, and were considering making the changes. I also revisited the instructions provided on the site. It appears I missed/skipped a step that I misunderstood. The necessary step I missed was to wipe the phone after the nandroid backup, but before the installation of the HTC image, or the CynogenMod ROM.
My initial experience with CyanogenMod was extremely positive, the phone seemed prettier and had tons of new functionality. The one issue that remained was a speed issue. I began uninstalling apps, and things seemed to get much better, despite the fact that CyanogenMod has APP2SD to store applications on an EXT2/3/4 partition on the SD card.
Everything has seemed to work extremely well over the past few weeks as I have used and played with the new rom. I have also upgraded to 4.1.9999 in the past day or two. Today when I attempted to connect to my S9 headset and play music, I have experienced some halting, and the music application crashes. I will wait for the next, allegedly more stable, release from Cyanogen, and hopefully this final issue will be resolved.