yes, Id assume PORT A is 28:1 = microKONTROL MIDI 2
the issue is, that is an assumption…and this is where things tend to break down 
it looks like it is connected properly , see:
=================================================
ACONNECT
client 0: 'System' [type=kernel]
0 'Timer '
1 'Announce '
Connecting To: 15:0
client 15: 'OSS sequencer' [type=kernel]
0 'Receiver '
Connected From: 0:1
client 28: 'microKONTROL' [type=kernel]
0 'microKONTROL MIDI 1'
1 'microKONTROL MIDI 2'
Connecting To: 128:0
Connected From: 128:1
2 'microKONTROL MIDI 3'
client 128: 'Pure Data' [type=user]
0 'Pure Data Midi-In 1'
Connected From: 28:1
1 'Pure Data Midi-Out 1'
Connecting To: 28:100:
what we are interested in is:
client 28: ‘microKONTROL’ [type=kernel]
1 'microKONTROL MIDI 2’
Connecting To: 128:0
client 128: ‘Pure Data’ [type=user]
0 'Pure Data Midi-In 1’
Connected From: 28:1
this shows pure data is listening on 128:0 (Pure Data Midi-in1) and is connected to 28:1 (microKONTROL MIDI 2).
(this information is kind of duplicated, in that we can see what the device is connected TO, and what PD mid input is connected FROM)
hmm, ok, heres what I would do:
a) change the alsaconfig to each one in turn… and reboot organelle after change it
(there is a different way to do this, but I dont want to get this ‘wrong’, so rebooting is ‘fail safe’)
b) after reboot start a patch , lets use C&G basic poly
c) take a Diagnostic log (this will allow us to see (a) has been effective), if you look at the first lines, you will be able to see the above, and be able to check for yourself
d) double check the midi channel on the Kontrol and MIDI-Config.txt are correct, Id go for channel 1
e) now try different things on the microKontrol e.g. different configs to try to use MIDI IN/PORT A/PORT B
(that includes sending MIDI thru the MIDI DIN ports on the microKontrol if possible)
f) if you have a hdmi monitor/keyboard etc, then I would connect those, and then use the PD “test audio and midi” function.
g) confirm the USB midi adapter is working over alsa, so we know alsa is work ok.
I have multiple port devices working fine here, and the microKONTROL is reporting itself as a class compliant USB midi device, so I see no reason why it shouldn’t work.
Its possible its something to do with the alsa/kernel version on the organelle (vs mac), but frankly that seems unlikely…
long shot… so after you have tried all the above…
another thing you can try to do, is to plug the controller in, after organelle is powered up, but just before you start the patch… then after you start the patch , take a diagnostic log…
this will enable us to see the initialisation messages from the driver (in dmesg), perhaps an error there… but this seem unlikely, given ALSA appears to be perfectly happy with the driver.
hmm, I cant think of what else to try… If I had the controller here, id do things like get alsa to dump the midi messages, test it on another linux install, in case there is some kind of microKontrol ‘quirk’ that has not been included in the organelle kernel yet - but these are things I cannot walk people thru.
I have had my organelle a while and have recently got a Microkontrol to use as a controller but it does not appear to “plug n play” with my organelle. I can see that this has been discussed here and 
what am i doing wrong?