It can take anywhere from a couple hours to several days to issue the e-ticket. This month I waited four or five days for one upgrade to ticket. We had a thread on this issue recently that might offer more insight. If everything is confirmed and they've told you the upgrade is queued for ticketing, I generally wouldn't worry (and you can ignore the fearmongering messages about how the reservation will be cancelled that always appear in MMB even after you've told them to issue the ticket). Although in your case there have been some complications along the way, so I wouldn't see any harm in calling them periodically just to make sure it's still in the ticketing queue.