Are you saying the HD rig is new? or has it worked perfectly in the past?
The first thing I'd do is eliminate the uad card, re-seat your HD Core, re-seat your RAM, trash your prefs, check all your cables, create a new session, import the tracks from the session that gave you trouble and see what happens.
If there're no problems, install the uad card. see what happens.
Unfortunately, there're so many variables these days it's hard to pinpoint a solution.
Pops and clicks usually means a 'clock' problem, but a spitting sound, who knows.
Is it random or always at the same spot on the the same audio file? on all audio files?
anyway good luck, welcome to ProTools, start honing your trouble shooting chops.