So I installed a module on my staging environment and all worked fine. However installing it on the live site hit a SQL error in one of the many upgrade files.
So I set the module XML files to false and, same error. Same error code too which I thought was not possible with Magento (I remember error codes being unique always).
Va SSH I've cleared the cache, compiled, disabled compilation, disabled caches, deleted the entire var directory after making a backup even and deleted the module files.
Still the error shows the same error code to the same file, a file that no longer exists, after deleting the var directory, the error file doesn't even exist, its like its stuck thinking it needs to show an error that's not happening (Though when I load the page for a split second I do see a var_dump of something).
The site has a massive database and file structure that restoring the last backup for everything to clear the issue will take about an entire day so I don't want to have to use that last resort.
EDIT
The error in question is
a:5:{i:0;s:228:"Error in file: "/home/runway/public_html/app/code/local/Ebizmarts/SagePaySuite/sql/sagepaysuite_setup/mysql4-upgrade-3.0.11-3.0.13.php" - SQLSTATE[42S21]: Column already exists: 1060 Duplicate column name 'base_surcharge_amount'";i:1;s:862:"#0 /home/runway/public_html/includes/src/__default.php(7842): Mage::exception('Mage_Core', 'Error in file: ...')
#1 /home/runway/public_html/includes/src/__default.php(7634): Mage_Core_Model_Resource_Setup->_modifyResourceDb('upgrade', '3.0.11', '4.1.7')
#2 /home/runway/public_html/includes/src/__default.php(7517): Mage_Core_Model_Resource_Setup->_upgradeResourceDb('3.0.11', '4.1.7')
#3 /home/runway/public_html/includes/src/__default.php(7432): Mage_Core_Model_Resource_Setup->applyUpdates()
#4 /home/runway/public_html/includes/src/__default.php(30269): Mage_Core_Model_Resource_Setup::applyAllUpdates()
#5 /home/runway/public_html/includes/src/__default.php(30195): Mage_Core_Model_App->_initModules()
#6 /home/runway/public_html/app/Mage.php(684): Mage_Core_Model_App->run(Array)
#7 /home/runway/public_html/index.php(90): Mage::run('', 'store')
#8 {main}";s:3:"url";s:1:"/";s:11:"script_name";s:10:"/index.php";s:4:"skin";s:7:"default";}
EDIT 2
Looks like I'm now able to access the entire site bar the homepage which still has the error page stuck on it.