Okay, so perhaps I'm the only person who cares about this, but I found a working, permanent solution to the CPU affinity problem and it's surprisingly simple.

Blizzard has basically already thought about this and added a setting. In the WTF\Config.wtf file, all your system settings are here. On mine, I found a line:
[code:1]SET processAffinityMask "3"[/code:1]
Call me crazy, but since it defaults to using CPUs 1&2, that mask looked like a binary number to me... Sure enough I set that to "12" and now my main WoW instance runs on CPUs 3&4 with no intervention from me.

For those not binary-literate:

CPU-1 = 1
CPU-2 = 2
CPU-3 = 4
CPU-4 = 8

Add up the values of the CPUs you want to utilze and that is the value to set in the Config.wtf file. For my soloing instance of WoW I set this value to 15 and it does seem to set affinity to all four CPUs. (Although I don't the my CPU is my bottleneck when running only one instance.)

Okay, so one main annoyance out the window.

UPDATE: Maybe it's just coincidence, but system just crash while running on all 4 CPUs. Maybe there's a reason they only use two? Oh well, at least now I can control WHICH two.