Okay, y'all, I don't know if Windows is fixed yet. I did an Ubuntu Live CD. You run Ubuntu directly from the CD, no permanent install on the computer. Did that and ran the Linux version of the AlphaRevX and everything worked PERFECTLY! S-OFF achieved, rooted programs installed, everything is good to go.
Not sure about the OTA yet. On the old Inc, once you did the rooting, your phone wouldn't get the OTA's yet, but not sure in this case. I'm pretty sure once you install custom ROM's, you're in the clear.
I'll let you know more when I find out. So for now, run the Linux Live CD and you're good to go.