On a Raspberry Pi 2, with 8 organ stops pulled, typically you can expect a note to respond fully in about 10 milliseconds. Technically this means the Midi <tt>note_on</tt> message has been transmitted on all 8 Midi channels.
To relate this to a normal organ playing experience, something like a 50ms 'attack time' would normally be deemed acceptable with a tracker action, though clearly this will always be a bit subjective. (If interested [http://www.pykett.org.uk/the_physics_of_organ_actions.htm The Physics Of Organ Actions] talks about this topic some more).
If you would like to review the latency you are experiencing in Box Of Stops, please take a look at the [[Logging output]].