1. Ok, I'll take a look. I hadn't originally designed it with WPMU in mind. If it's a fairly simple fix I'll get it in there.
2. It is there for debugging when/if needed. It wasn't meant to be a public-facing feature and is not meant to be used full time, thus, this is as intended.
3. Yeah, this is a known issue and why the plugin hasn't seen a 1.0 release. The only real guaranteed to this is to take a fairly different approach to getting the function list, which likely involves either forgoing the use of get_defined_functions() or some level of hackery. The plugin won't see a 1.0 release until that is solved, but it is unfortunately not a problem I have time to solve at the moment.
