magento cron schedule not working, no heartbeat - php

Question

I have inherited a magento site and the cron schedule does not work. It was set in magento with */5**** and the same in cpanel. I installed AOE Scheduler and all the emails that had been stuck in the queue came through but now I just get a message "Last heartbeat is older than XX". If I run the scheduled tasks manually the emails come through but I get a "405 Error - Not Allowed" page and I find all my file permissions have been changed to 666 (the number of the beast). I have been setting my file permissions to d - 755 and f - 644 but depending on which forum you read this could be wrong. Please help, I have been on this for days.
This is my cron.php
<?php
// Change current directory to the directory of current script
chdir(dirname(__FILE__));
require 'app/Mage.php';
if (!Mage::isInstalled()) {
echo "Application is not installed yet, please complete install wizard first.";
exit;
}
// Only for urls
// Don't remove this
$_SERVER['SCRIPT_NAME'] = str_replace(basename(__FILE__), 'index.php', $_SERVER['SCRIPT_NAME']);
$_SERVER['SCRIPT_FILENAME'] = str_replace(basename(__FILE__), 'index.php', $_SERVER['SCRIPT_FILENAME']);
Mage::app('admin')->setUseSessionInUrl(false);
umask(0);
$disabledFuncs = explode(',', ini_get('disable_functions'));
$isShellDisabled = is_array($disabledFuncs) ? in_array('shell_exec', $disabledFuncs) : true;
$isShellDisabled = (stripos(PHP_OS, 'win') === false) ? $isShellDisabled : true;
try {
if (stripos(PHP_OS, 'win') === false) {
$options = getopt('m::');
if (isset($options['m'])) {
if ($options['m'] == 'always') {
$cronMode = 'always';
} elseif ($options['m'] == 'default') {
$cronMode = 'default';
} else {
Mage::throwException('Unrecognized cron mode was defined');
}
} else if (!$isShellDisabled) {
$fileName = basename(__FILE__);
$baseDir = dirname(__FILE__);
shell_exec("/bin/sh $baseDir/cron.sh $fileName -mdefault 1 > /dev/null 2>&1 &");
shell_exec("/bin/sh $baseDir/cron.sh $fileName -malways 1 > /dev/null 2>&1 &");
exit;
}
}
Mage::getConfig()->init()->loadEventObservers('crontab');
Mage::app()->addEventArea('crontab');
if ($isShellDisabled) {
Mage::dispatchEvent('always');
Mage::dispatchEvent('default');
} else {
Mage::dispatchEvent($cronMode);
}
} catch (Exception $e) {
Mage::printException($e);
exit(1);
}
This is my cron.sh
#!/bin/sh
# location of the php binary
if [ ! "$1" = "" ] ; then
CRONSCRIPT=$1
else
CRONSCRIPT=cron.php
fi
MODE=""
if [ ! "$2" = "" ] ; then
MODE=" $2"
fi
PHP_BIN=`which php`
# absolute path to magento installation
INSTALLDIR=`echo $0 | sed 's/cron\.sh//g'`
# prepend the intallation path if not given an absolute path
if [ "$INSTALLDIR" != "" -a "`expr index $CRONSCRIPT /`" != "1" ];then
if ! ps auxwww | grep "$INSTALLDIR$CRONSCRIPT$MODE" | grep -v grep 1>/dev/null 2>/dev/null ; then
$PHP_BIN $INSTALLDIR$CRONSCRIPT$MODE &
fi
else
if ! ps auxwww | grep "$CRONSCRIPT$MODE" | grep -v grep | grep -v cron.sh 1>/dev/null 2>/dev/null ; then
$PHP_BIN $CRONSCRIPT$MODE &
fi
fi