I look forward to seeing how you get on!
Interesting about the glitches - I read somewhere that either the 2408, 168RC or ADAT can be the master clock source - which one are you using? There's some tech info on the MOTU site about this I think related to ADAT sync problems..
Also as you have a black face (44.1 khz) ADAT - I remember that it doesn't clock at exactly 44.1 khz but 44.110 or something like that - I wonder if that's the cause of those clicks ??? ..so maybe word clocking would cure it? (just a guess as I'm not an expert!)