Here's the update with my steps and results, as per the other forum:
https://forum.litecoin.net/index.php/topic,2924.msg44380.html#msg44380Essentially it was as easy as git cloning to a different directory, compiling with the options I wanted, and then Lantis (from litecoin forum) suggested to keep it simple by modifying the common.pl script to point to the new cgminer. I liked this method because if something went wrong, you can simply comment a line out and get back to mining.
The system is now enjoying cgminer 3.4.2 (thanks ckolivas/kano!) with slightly increased performance.