Device is dead?

Greetings,

I'm stuck in a very bad place with my Nexus 6 and was hoping someone could help me out of it. I obviously made a grave mistake in doing this so I'm hoping all is not lost. Here are the steps I performed that got me into this mess:

1) Downloaded the latest root .zip file from Chainfire, which notably, does not have a 6.0.
2) Flash Stock ROM to the device Marsh mellow 6.
3) Phone booted up just fine, I then unlocked developer options and then selected allow oem updates.
4) performed a reboot to the bootloader.
5) This is where I went wrong: executed the root-windows.bat script.

Now when the device boots I get an error stating the device is corrupt and cannot be trusted and it immediately shuts off. What I'm trying to do is figure out how to get the device to the point where I can flash the stock 6.0 rom back to it but I keep getting the error message stating I must turn on allow oem unlock, but to do that the device has to boot up to allow me to select that setting and I cannot do that.

Please help, I feel like I've really screwed this device up and I'm hoping one of you very smart folks can help me out of this mess.

Thanks!

Eric