I found I was getting syntax errors when running this script against v0803 db. Turns out the mysql db admin pgm told me there was a syntax error in the script.
The problem is on line 45, the quote characters were missing on the field names - here's the updated syntax:
INSERT INTO `
project_user_permissions` ( `user_id`, `project_id`, `permission_id` )
FYI I took the contents of the 0803-086.php files, replaced
with my table prefix and ran it as an sql script against the database.
After that - it converted perfectly.