Re: functions.php and bp-custom.php
You should set your slugs in wp-config.php
Comments should be fine in bp-custom.php – there must some error in the way you have the file set up
Ps you are right that functions.php is theme specific, and bp-custom.php is install wide. However there are also order of invocation issues.. They don’t happen at the same place in the initialisation.
For slug and URL mods have a read of the documentation on here