Couple things. First, you need to make sure you have both a user #1, the placeholder user, and a user #2, your main admin. You can check both of these by running this query and see what you get back:
SELECT U_Number,U_Username FROM w3t_Users WHERE U_Number IN('1','2')
If either of those are missing, that could be part of the problem. We can check a few other things from there, however any of the old deleted PMs aren't recoverable unless we get you to restore to an old db prior to the upgrade and work out the initial problems.
