Once you upload tools.php, you need to run it from your browser lol, my bad as i didnt specifically tell you that, but it works just like any other.
yourdomain.com/forums/admincp/tools.php
The problems were caused by you, not the vb upgrade.
You also need to look at the tables and see what ones are actually used, the tables with or without data, if the vb3_ tables are not empty, then you need to correct your config.php to use them or the non-prefixed tables.
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