Many, many thanks, William! I had been working with Apple Customer Care to try to get early access to the 10.9.2 beta to see if it fixed my problems (I have four days left to decide if I want to return my new Haswell iMac for a refund), but they couldn't figure out how to make that happen without me paying to join the Apple developer program.
I installed 10.9.2 and it's made the problem much, much better... but has NOT fixed things completely. I still get an occasional pop or click, but nothing like it was with 10.9.1.
Does anyone know whether folks with Fusion Drive Haswell iMacs BUT Firewire audio interfaces are experiencing the same problems? I have a Presonus Firepod that's Firewire-based, but it's incompatible with Mavericks, so testing with that wouldn't be terribly helpful. Yesterday I purchased an Apogee One for iPad and Mac to see if it would eliminate part of the problem since Apogee said it had few enough channels that it didn't suffer from the problem (unlike their Duet and higher-end interfaces).
So, now my fear is that Apple will think 10.9.2 fixes the problem "enough" and never gets around to fully fixing the Fusion Drive problem. It would seem there should be some Unix configuration file buried somewhere deep down in OS X where the end user could tweak the behavior of the Fusion Drive's "smarts" to have it be less aggressive in swapping files around while the data bus is being strained by other processes (like Logic). At least that's what I assume if causing the Fusion Drive related problems. I know there is a separate USB 3.0 issue, but it seems that's on the audio interface vendors' plates to work around.
Thanks to all who have helped debug and (almost) solve this problem.