Also, I'm making a stock ftf for myself.
I believe the issue is resolved - I did things a little differently this time...
1 - flashed the CWM via flashtool
2 - flashed superSU in CWM, activated superSU Pro
3 - installed busybox pro to /xbin and declined whatever funny business it was asking about at first (something already in /sbin)
4 - rebooted
5 - let some apps update, etc., then shut the phone down
It's staying off! Hopefully that's the end of that issue..