The line I commented out to actually get the indexer to work and finish was line 285 in app/code/core/Mage/Catalog/Model/Resource/URL.php
Before
Mage::logException($e);
Mage::throwException(Mage::helper('catalog')->__('An error occurred while saving the URL rewrite'));
After
//Mage::logException($e);
//Mage::throwException(Mage::helper('catalog')->__('An error occurred while saving the URL rewrite'));
I hope its work for you.