ac3filter should have a control panel console. Open that up from your system control panel and it's got a volume control. AC3 is normally normalized a bit lower than stereo sound (to give a wide range of sound without clipping), so you've gotta compensate for it.
Also, ac3filter can also change how the audio is played back (like, if you've got stereo speakers versus 5.1 audio). If you're trying to play back dolby digital and all you've got is stereo speakers, you'll lose a lot of signal that's supposed to be going to the other 3 speakers.

Edit: and to answer the other two questions:
1: We don't really intend to go back and re-release mzero episodes with new audio, they're done and we're happy with them.
2: We aren't really sure what's going on with ongoing stuff right now. I know there's some work being done on that accursed Guardian Hearts, but MZ is kind of up in the air for the last episode... but either ANBU will do it or we will, probably.