I used to be subject to those middle of the night call-ins. I don't miss them a bit. You have my sympathy.
I'm interested in your comment "bearings themselves still had lube". I thought the spindle bearings were lubricated by the oil cups inside the body of the mill. When I oil mine there, the oil runs out of the spindle in front and back. Did yours have some sort of grease or something? Good luck with the re-assembly.
I was called in to work at 2:30 AM for a few hours and just got up. Now I gotta find some coffee.