the channel issue is at the JACK/ALSA level. You are probably telling JACK to open a device that, as far as the device driver is concerned, has only 2 channels. You should use aplay -L to see what other device names you have that you could potentially tell JACK to use. Once you get the right device name, JACK will see as many channels as that device has. You need to understand that ALSA likes to present the device “as it really is”. This means that there are ways to access it as if its a 2 channel interface, and other ways that (might) have more channels.
do you understand what MTC is? you haven’t indicated that you have any gear that would actually send/received MTC. either way, you need to go to Preferences -> MIDI to check which port is being used for MTC and then use the MIDI tab of qjackctl to connect that port to wherever MTC is coming from/going to.