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Normally you do that kinda of thing through fastboot (accessed either through a hardware key combo on boot or through 'adb reboot fastboot' while booted. Then you boot into your recovery and flash your SuperSU binary (for root) and GApps (for play store etc). Then you boot as normal and immediately turn on ADB for when you break it again...
hamrack
Ok, I think I had this wrong. Can anyone confirm... I have to flash the new radio and ROM images via ADB command line right?
Still can't remember when and how I gain root access, but that's no so important at the moment.