I don't see any .conf files. I could try to uninstall and reinstall but I am not sure which step the .conf file would have been created.
...
Would it have been in the ./configure --enable-gekko step you think?
No, there's a save configuration option in the CGMiner UI. That is what would create the configuration file. If you didn't find it then you may not have done that.
Uninstalling/reinstalling wouldn't help, I don't think. Sounds like you have some other issue.