Update:
I have no freezes in the past week, since I speed matched the cards in both slots: going to the 2000x cards in both slots seems to have eliminated the issue for me. Which is good, if annoying, because it seems a waste to have such a high speed card in the JPEG slot. Oh well.
For anyone collecting data, my freezes happened in the following AF Modes: Single Point, Single Shot and in 3x3 zone mode in Continuous Focus mode. In both cases, the drive setting was CL, which I have set to 5 FPS. Camera is permanently in boost mode.