Hello Harken,
Setting up 2 Motus (I did it a few times) linked by an ethernet cable usually works well, but to rule out any network problems, can you try/test by connecting some speakers to the MOTU connected (using USB) to the computer. Disconnect the ethernet cable from the MAIN (usb connected) MOTU during the test.
If you don't have glitches, then something is wrong with you network connection, MOTU configuration quite possibly. If you have glitches even with 1 MOTU only then have a look at Hauptwerk User Guide - Performance Tuning - starting at page 293. You will find a list of tweaks start page 308
Also have a look at this thread on our forum - https://forum.hauptwerk.com/viewtopic.php?f=4&t=15194
Also, disabling the service SYSMAIN/Superfetch (Win7) often solve audio glitches problems. Disabling Windows' page file also helps (see page 310)
Hope that helps.