Yes, to get per-key velocity on Misha, you need to trigger it with MIDI. MIDI velocity values are also stored in your tone rows.
You could also use a pedal that sends voltages to one of the CV in jacks and control velocity that way. (The velocity of a given keypress then would be defined by the voltage of pedal and not the keypress velocity.) This requires some setup in the Cv In menus- let me know if you have such a pedal and need help with this.
Currently, Misha does nothing with aftertouch, but they will pass through, so your receiving synth can use them.