Ducky - I’m not sure why the extruder heater would have stayed on but if you are running a makerbot replicator2 you have the wrong config. I think the config file you have now is pulled from upstream and is for original makerbots and clones, not rep2 and rep2x units. You need to pull the code and example config file from my repo (GitHub - dockterj/klipper: Adding support for MakerBot Replicator 2). Let me know if you need some help in the steps needed to do that.
You will need to reflash the mcu as well. I don’t know anything about using KIAUH to flash mcus - I’ll look into that but in general for the mightyboard rev g and h you have to flash at 57600. You may be able to flash it by powering down and up the board at just the right time but I haven’t looked into that.