I have a Remora Pro with a mag 3 as well. I can't really say anything about the breakin period because I bought mine used and it has been producing skimate since day one. I haven't had any problems with microbubbles entering the tank either. As for the noise, you might be out of luck... Mine is loud enough that I sometimes turn it off if I am watching a movie.
AquaC Remora Pro
140#s Live Rock from LiveRocks.com
Frogspawn, Hammer, Zoos, Leather Frag, and Xenia and Green Star Polyp frags from fishfreek and Alarmguy66, Thanks!
Member of the Unofficial A-Team