You might try to disable hooks, run your upgrade then enable the hooks when it complete, if it completes.
Add this to your config.php file just after the opening <?php tag.
define('DISABLE_HOOKS', true);
This will disable all your hacks while you do the upgrade. If the upgrade is successful comment the line out so you can start up with your hacks running. You may need to upgrade some or all of them before you are finished.