I can't help you with your jack problem but I can certainly help with pulseaudio. Removing pulse can be a big problem because so much is tied into it now. You can break things that don't even appear to be related. I just upgraded from Kubuntu 14.04 (Trusty) to 16.04 and, of course, pulseaudio took over my system and caused me all kinds of problems with jack, riffstation, and a bunch of other things (I've got an ICE1712 based sound card and external gear). The easiest and safest way to disable pulseaudio in Ubuntu is to open a konsole and do the following:removing pulseaudio