So, somehow this USB firmware infection can somehow load itself into your computer, once a infected usb device is plugged in. It would appear the USB hardware has the ability to load software into memory bypassing the OS, thereby causing the cpu to run the infection? So say you had Tails OS, or...
Have you tested booting with only the SSD?
If this was my computer, I would wipe the whole thing (all drives), and start all over, fresh install (not a restore or recovery). Its also a good test of your data backup (does it actually work).