I found a ridicilous mistake I had made. Majority of the jacks I'm using don't have switches, but 3 of them does. I had connected the ground wire to one of these 3, and accidentally soldered it to the "pin" of the switch, not the sleeve of the jack (I don't know the right word for the pin).
Anyway, now my MIDI out works fine. Still having a weird problem with the USB, though. When I connect the USB cable, Megadrum works fine for a while, but after about 30 seconds it suddenly stops sending any MIDI data. Reboot doesn't help, but after some time it works again.
Luckily I don't need the USB now, but ofcourse it's a little disturbing to know that it doesn't work.
Tomorrow I will update the new firmware which supports Yamaha 3-zone cymbals. Then I just need to configure it to work well with my pads and I think I'll be done. I'll post some pics and maybe a video clip when it's ready. Thank you for making this possible.
Oh yeah, and the LCD backlight is very dim, so I'll replace the 470 resistor with a smaller one.