Well, although a colossal PITA, the OTA is working fine now.
Started with stock rooted. Nothing modded or deleted.
Took forever to download and install - 16 hrs - needed a battery pull.
Ran OCR - Root Check said I'm not rooted. Then got the "SU binary out of date"; SU failed to update when I tried manually. Uninstalled SU (v3 with Elite add-on), reinstalled, now rooted OK. Problem here may be that OCR was pushing old SU v2 stuff to phone and corrupting my v3 install (?).
Battery at 90% after 7 hours at work with WiFi and push-Exchange (which is better than normal)
USB charging working fine.
There is obviously something flawed with this OTA. Prior ones were quick and easy.... It's good that Moto is starting to use a group of folks like us to beta test future updates to avoid releasing a screwed up OTA like this one..