I disabled the XF1 version and it placed all my private threads in moderation. Just upgraded to the XF2 version and logged in as a test user and all the threads are visable. Can also click into each thread and see all the discussion.
My back up is from XF1 - So i'm just re-installing that, then upgrading it to XF2.
I'll leave the XF1 version enabled before I upgrade to XF2.1
In regards to users - They should all exist. The only ones I delete are the spammers, and they don't usually make it to this part of the site. Got 92k posts in private threads 1, so would be difficult to go through and check.
I forgot to let everyone know that the errors were coming from the non-existent users as mentioned. The upgrade routine has been patched in the current version to account for that possibility and is on the download server.