I heard the rattling for the first time yesterday as I rolled through a McD's drive-thru. It just sounds like gear shafts moving around, possibly rattling within their bearings a bit. I've heard worse noises coming from a Chevy S-10 manual transmission. If any of you have ever driven one of those, you know that even brand new, there's so much slack in the transmission that you can hear the gears bang against each other whenever you change speeds.
Considering the type of transmission this is, there's likely not a lot that can be done about it. As for the surging / stuttering / indecisiveness, mine continues to improve with every drive. I guess I'm one of the lucky ones (knocking furiously on wood).