"Modyfying /etc/security/limits.conf should not be done on Ubuntu 10.04 and later"
True.
I'll wait for further advice about whether and how I should actually do anything about this particular setting…
Do nothing. Or, to convince yourself, just take a look:
cat /etc/security/limits.d/audio.conf
The fact is that the rtprio and memlock lines can be in
/etc/security/limits.conf or in any file under the directory
/etc/security/limits.d/. Nowadays, when jack is installed in your system (the jackd package)
/etc/security/limits.d/audio.conf is written, so you only have to add yourself to the audio group in order to run jack in realtime mode.
You already belong to the audio group (double-check with this command: "groups"). Otherwise, jack couldn't be run in realtime mode. As you are seeing jack as a realtime process, you get that part right.
A question: should Jack be higher priority or lower than the audio interface? RIght now, Jack is higher.
I am not sure about the right priority for jack but I think that it should be just below the audio card (not in exact numbers as "90 then 89", but in position as "audio card, then jack and nothing in the middle"). Anyway, feel free to experiment and maybe share your experience

About the glitches: I suggest you open a new thread with this particular problem. This one is bloated and very few people is following by now, I guess.
Bluetooth and wireless are possibly to blame, but who knows. You can start by unloading those particular kernel modules (See
lsmod to identify them and use
sudo modprobe -r some_module. To reload,
sudo modprobe some_module).
Another possible cause is what was already mentioned: Avoid CPU frequency scaling "on demand".
Probably, unbindig non-used usb buses in IRQ #18 would help too. Or a low-latency kernel. But try first the wireless and bluetooth modules unloading and the CPU freq scaling.
Cheers, Pablo