Extremely slow PHP loading after update

Hello Everyone! Today I've stumbled on something that I've been having a hard time figure it out. After the latest major cpanel update. The Story: Ok So the other week one of my staff members decided to add Cpanel Backups on the local server in the root LV partition (this partition only had 10GB which filled immediately). So I decided to add another drive of 50GB and added it to the LV group. doing this still without knowing it was the cpanel backups taking up the memory. So around 3 days later after the daily backups the drive was full and all websites stated that suspended due to resource limit. So I decided to see what was using 50GB and there I found the backups. I disabled the backups on the WHM (As you can still have access to it) then I deleted some of the old backup folders in the cpanel backup directory. after that all websites immediately started displaying 406 Errors So I had a look around and found it was ModSEC. I knew I don't currently need modsec so I re-compiled apache without it. which restored everything except.. Websites that contain PHP. and this is where I am at. I've look around and couldn't really find anything useful and done some troubleshooting but still to no avail. if I'm extremely lucky it will load before the timeout but that could be 20-50 Seconds I'm running cloudlinux. [LIST]

CLOUDLINUX 6.7 x86_64 vmware " web [LIST]

WHM 54.0 (build 8) [LIST]

Load Averages: 3.26 3.19 3.05 Here is that last few things from /var/log/messages
Feb 1 17:46:48 web lvestats-server[1910]: : no such table: history Feb 1 17:47:45 web PAM-hulk[22609]: Brute force detection active: 550 LOGIN DENIED -- TOO MANY FAILURES Feb 1 17:47:45 web PAM-hulk[22610]: Brute force detection active: 550 LOGIN DENIED -- TOO MANY FAILURES Feb 1 17:47:45 web PAM-hulk[22612]: Brute force detection active: 550 LOGIN DENIED -- TOO MANY FAILURES Feb 1 17:47:48 web lvestats-server[1910]: : no such table: history Feb 1 17:48:48 web lvestats-server[1910]: : no such table: history Feb 1 17:49:48 web lvestats-server[1910]: : no such table: history Feb 1 17:50:03 web pure-ftpd: (?@127.0.0.1) [INFO] New connection from 127.0.0.1 Feb 1 17:50:03 web pure-ftpd: (?@127.0.0.1) [INFO] __cpanel__service__auth__ftpd__G33PiRVfgif9nDGqHzp6o08en0M46WkbW3tBqu64fzMZg__iKlEYgo5KlRk4dHqK is now logged in Feb 1 17:50:03 web pure-ftpd: (__cpanel__service__auth__ftpd__G33PiRVfgif9nDGqHzp6o08en0M46WkbW3tBqu64fzMZg__iKlEYgo5KlRk4dHqK@127.0.0.1) [INFO] Logout. Feb 1 17:50:48 web lvestats-server[1910]: : no such table: history Feb 1 17:51:48 web lvestats-server[1910]: : no such table: history Feb 1 17:52:48 web lvestats-server[1910]: : no such table: history Feb 1 17:53:48 web lvestats-server[1910]: : no such table: history Feb 1 17:54:48 web lvestats-server[1910]: : no such table: history Feb 1 17:55:04 web pure-ftpd: (?@127.0.0.1) [INFO] New connection from 127.0.0.1 Feb 1 17:55:04 web pure-ftpd: (?@127.0.0.1) [INFO] __cpanel__service__auth__ftpd__Ep5FBYdwOe0LjmHPoUHi51QMvSV2olshZb1g3ddPlq8elrKUD8g8YMYCoDr_o6Ly is now logged in Feb 1 17:55:04 web pure-ftpd: (__cpanel__service__auth__ftpd__Ep5FBYdwOe0LjmHPoUHi51QMvSV2olshZb1g3ddPlq8elrKUD8g8YMYCoDr_o6Ly@127.0.0.1) [INFO] Logout. Feb 1 17:55:48 web lvestats-server[1910]: : no such table: history Feb 1 17:56:49 web lvestats-server[1910]: : no such table: history Feb 1 17:57:49 web lvestats-server[1910]: : no such table: history Feb 1 17:58:49 web lvestats-server[1910]: : no such table: history Feb 1 17:59:49 web lvestats-server[1910]: : no such table: history Feb 1 18:00:05 web pure-ftpd: (?@127.0.0.1) [INFO] New connection from 127.0.0.1 Feb 1 18:00:05 web pure-ftpd: (?@127.0.0.1) [INFO] __cpanel__service__auth__ftpd__Pc3Al1iqDfQtYJjr7Lt3daSkgr6ZLX4B8Su4EbgZjp6H3Wvs3lPvD7vKatFZKmgx is now logged in Feb 1 18:00:05 web pure-ftpd: (__cpanel__service__auth__ftpd__Pc3Al1iqDfQtYJjr7Lt3daSkgr6ZLX4B8Su4EbgZjp6H3Wvs3lPvD7vKatFZKmgx@127.0.0.1) [INFO] Logout. Feb 1 18:00:49 web lvestats-server[1910]: : no such table: history
df -h
root@web [~]# df -h Filesystem Size Used Avail Use% Mounted on /dev/mapper/vg_web-lv_root 74G 47G 24G 67% / tmpfs 3.9G 0 3.9G 0% /dev/shm /dev/sda1 477M 121M 331M 27% /boot /dev/mapper/vg_web-lv_home 439G 27G 391G 7% /home /usr/tmpDSK 2.0G 68M 1.9G 4% /tmp root@web [~]# nano /var/log/messages
This is really the only interesting thing in Apache log
[Mon Feb 01 17:49:15.274274 2016] [:error] [pid 11249] mod_hostinglimits:Error on LVE enter: LVE(506) HANDLER(application/x-httpd-php5) HOSTNAME(MYWEBSITETHATIREMOVED.tld) URL(/pwreset.php) TID(11249) errno (7) Read more: http://e.cloudlinux.com/MHL-E2BIG min_uid (500) [Mon Feb 01 17:50:04.832514 2016] [core:error] [pid 20175] [client IPADDRESSREMOVED:52858] Script timed out before returning headers: index.php
You Help is muchly appreciated.