I'm not meaning to question your earlier statements, but, from your descriptions of what is happening, I'm wondering if your problems might be more the result of running PHP5 than of the MySQL version.
Many "older" scripts are written in such a way that they need to be changed to work properly with PHP5. It could also be something as simple as the setting of register_globals or some other setting that is changed, by default, with PHP5.
I suggest you try to run the script with your domain set to use PHP4, and see if you have better luck. It just may solve your problem. .
You can change the version of PHP your domain uses in the control panel from the Domains-->Manage Domains screen - just click the "edit" button next to the domain, and check the radio button for PHP4.
You can always change it back if it doesn't help. Good luck, and Merry Christmas.