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BF-2 (volume issue)

That third pot is the clock frequency adjust - not gain. Don't muck with it unless you know what you're doing - it will not affect the gain of the pedal but it may stuff up the bucket brigade device operation - which is bad!

Most boss chorus and flanger units have a slight volume boost designed to enhance the impact of the effect. This is part of the reason that the Boss CE-2 is loved by guitarists.

It is possible to modify the unit, but it's not trivial unless you have some electronics knowledge and soldering skills. If you're keen to go further, I would suggest you visit DIYStompboxes and search for topics on the BF-2.