The plot thickens... on some boots I've noticed that the freezing that seems to occur is really the phone not displaying the app or utility I just opened. As an example, I opened the drawer and chose Voltage Control, the usual popup indicates that it has been granted super user permission, but the screen continues to show the drawer. When I press the home button it shows the Voltage Control window, but I can't interact with it. This behavior was been consistent during this last boot, but at least I'm able to rotate the screen so it redraws. Changing the CPU to 480 mhz makes no difference with this issue.
This last boot seems to be working much better, though. I've been able to do more stuff in the Play store without it closing on me. Maybe reinstalling CWM, clearing everything but the SD card, and reflashing did the trick.