In Yamaha type 3 zone cymbals, the edge switch is connected over a 10k resistor and the bell switch is connected directly. Thus the edge Threshold MUST always be higher then 3rd zone Threshold (BThreshold). If not, then only the 3rd zone hits will be registered when you hit edge or bell. Read about BThreshold in relation to edge Threshold in
http://www.megadrum.info/content/pads-settings right at the bottom.
Note that in genuine Yamaha 3 way cymbals there is no separate choke switch - you choke by pressing the edge area where the edge hit switch is located ( or by pressing the bell switch area)
Normally, with Gain 4, Threshold on the Edge should be in the 20-30 range, and the 3rd zone Threshold (BThreshold) in the 0-5 range.
I suggest you to start with the 3rd zone Threshold (BThreshold) set to 0 and the edge Threshold set to ~40-50. Start lowering the edge Threshold by 1 at a time (make sure MDM and MegaDrum are always in sync, e.g. by enabling LiveUpdates) while pressing and releasing the edge hit switch (not the choke switch) and monitoring data in the MIDILog. There will be a point when you will reliably be getting Aftertouch On messages each time you press the switch and Aftertouch Off each time you release the switch. This is your Threshold for the edge.
After that you start raising 3rd zone Threshold (BThreshold) by 1 at a time while pressing and releasing the bell hit switch and monitoring data in the MIDILog. There will be a point when you will reliably be getting Aftertouch On messages each time you press the switch and Aftertouch Off each time you release the switch. This is your Threshold for the bell (3rd zone).
There is still the possibility that MD isnt wired properly as well. Dmitri?
Judging by what settings you were trying up till now I think this is very unlikely. You could test the cymbal in another input to verify this.
What of my questions earlier about the pedal jack, given my leads are good.
I'm not sure what to say. You can open up the case and check the continuity on the pedal jack. But again I doubt there is anything wrong with it.