Thanks for the offer , i may well be contacting you soon , however i will persevere and try to figure out some of the issues myself , a few of them are irrelevant like the roundcube and the missing script ..
I have found the issue with the Mod Security issue
Original fault when installing Mod Security with Comodo or WASP rules was :
Starting httpd: httpd: Syntax error on line 507 of /usr/local/apache/conf/httpd.conf: Syntax error on line 5 of /usr/local/apache/conf.d/mod_security.conf: Cannot load modules/mod_security2.so into server: /usr/local/apache/modules/mod_security2.so: undefined symbol: apr_crypto_block_cleanup
[FAILED]
When i had a look at /usr/local/apache/conf.d/mod_security.conf file i found this entry :
<IfModule !mod_security2.c>
LoadModule security2_module modules/mod_security2.so
</IfModule>
Notice the ! in the first line , once this was removed , apache started successfully , how this excalamation mark got there is beyond me as i have never altered this file before ??
Regarding the phpmyadmin blowfish secret , could you tell me where the new location is for this file as admin stated the old location is no longer in use ??