1) When a 2Pac becomes a zombie, is there a way to restart it without having to manually unplug the USB device? Is there a parameter in cgminer, or USB Management setting that will do this for you?
I haven't been able to restart a zombie without a replug. I intend to build a relay board controlled by the Pi3's GPIO pins so I can have a script detect a zombie and replug it automatically.
2) Is it possible to configure different frequencies for each 2Pac attached to the computer?
Not with a single instance of cgminer. cgminer takes a single --gekko-2pac-freq parameter and applies it to all detected sticks. It might be possible with multiple instances of cgminer and a cgminer.conf for each to limit which 2pacs a particular instance of cgminer controls, but with the cgminer conf Write function currently broken I haven't played with this. Oh, and I also only have one 2Pac at present.