SmartFAQ is developed by The SmartFactory (https://www.smartfactory.ca), a division of InBox Solutions (https://www.inboxsolutions.net)
"Warning: copy(../mainfile.php): failed to open stream: Permission denied
Likely you don't have access to your mainfile.php on your server. Contact your host and ask them to make it writeable until after your install finishes.
If you are trying to edit the theme.html in your themes folder and nothing seems to be changed, be sure that you set "Update module template .html files from themes/your theme/templates directory?" to "YES" in General Settings!!