1. Threshold on the 3rd zone MUST always be lower than Threshold of the Edge Input. Also, if it is a 3 way Yamaha cymbal, all 3rd zone notes must not be zero. These two combined is the reason why you seeing C-2 in your MIDI logging. Btw, MDC has built-in MIDI Log with Raw output which shows all MIDI data, not just note names. If it a dual zone cymbal set notes in 3rd zone equal to notes of the Edge input.
2. How did you do the configuration of the cymbal? It seems like you left Threshold on the Edge at default and I doubt it is the right Threshold level of the switch (Edge) input for your cymbal.
3. All the levels (except Low and High) in the Pedal settings are at 0. It is perfectly ok provided you use CC messages for pedal positions in your VST. Is this the case?
Just blindly copying somebodies settings without some understanding what they mean may cause more problems than when configuring these settings from scratch on your own. I'd suggest you to read settings descriptions in
http://www.megadrum.info/content/megadrum-configuration