Ok, hope this helps someone.
Had a devil of a time with 10.12.2.
• Update via MAS went smoothly
• First reboot kernel panic -> reboot
• Had to boot clover with nv_disable=1
• Installed latest nvidia web drivers
• Next reboot, again panic reboot
• Next boot, booted to black screen
• Was able to ssh into system and poke about, so clearly a Nvidia issue
• Edited /S/L/E/AppleGraphicsControl.kext/Contents/Plugins/AppleGraphicsDevicePolicy.kext/Contents/Info.plist
• Seems update "reverted" changes to MacPro key Mac-F60DEB81FF30ACF6 back to "Config1"
• Changed to "none"
• touch /System/Library/Extensions
• rebooted
• All good now or same as before upgrade for a X99 system - nackered USB3, ALC1150