So I worked through the issue, the E Stop was up, and I had every process turned off and USB unplugged. I could still not remedy the issue on my primary system. I ended up having to use a separate Surface Pro Notebook to flash the firmware.
My guess is that the MSI Z490 motherboard has some sort of driver for the LEDs that is interfering with how the SC2 interfaces. As even with removing the MSI bloatware I could not completely wipe LEDKEEPER.EXE without editing the registry.