Hi Casey,
I've managed to reflash the chip after a bunch of tries.
Initially reflashed it back to the backed up original firmware. Then went ahead to check functionality in Windows and it won't see the ports at all. Curiously enough, USB-C devices worked while with Elias's firmware, USB-C wasn't working.
Thunderbolt didn't work though. I can see it in Device Manager but ports are not seen.
Went back and reflashed it to NVM33, checksum was good.
Booted back to OSX and Thunderbolt BUS shows the same thing.
Also worth mentioning, USB-C doesn't work on OSX either, with NVM33 installed.
Here's a picture of IOREG.
View attachment 460366