For what it's worth, if you can't get the wifi problem fixed, you can flash the 4.1.2 fastboot via rsdlite (or Matt's utility might have it - haven't looked in awhile), and that clears it up. So evidently it was some sort of problem when the OTA was patching files and not an inherent issue with 4.1.2 (also evidenced by the small percentage of users having the issue).
Obviously if you're rooted running 4.1.2, you'll lose root if you do this and there's currently no way to root 4.1.2, which is also necessary to unlock your bootloader. But I had to have wifi and I'll just hope for a 4.1.2 exploit in the future! If you decide to go this route, also know it wipes your phone completely.
My experience with this WiFi problem backs up your conclusion. I just received my handset back from MoTo and they included more details on their findings. They indicated the following:
PROBLEM FOUND: No Functional Fault Found
REPAIR ACTION: Reprogramming/Reflash/MR/MC
This is what I fully expected, since the behavior observed on the handset supported it as the likely cause, i.e. WiFi worked perfectly fine immediately before the OTA and would not work at all immediately following the OTA.
While it's not convenient to have gone through the hoops of sending the handset back to MoTo for the repair, I feel it's worthwhile so they get to see the problem firsthand and can hopefully work to avoid it in future updates.