I think maybe the term manual seems to be mixed up. By manual in our instructions for the tp_upgrade.php, we mean that you have to run the file in your browser by uploading it to your forum root directory (where SSI.php is). Then you run that file in your browser "manually" by hitting it in your address bar. http://www.yourdomain.com/path_to_forum/tp_upgrade.php
It's better to run the do_hooks and tp_upgrade files first. But it shouldn't matter as long as you complete all the steps. If you are running the tp_upgrade.php file "manually" and it is not inserting all the tables into your database, there is a problem somewhere else that needs to be found if you want it to work on your server.
Manually inserting the tables and structure (in the way that we've done in this topic) will not solve the problem because of the settings that need to be inserted into the new tables will not be there, and you will have lots of errors if those settings are not there.