Hope the following may be of use to somebody...
Heres where I now am. The webserver runs direct from an original knoppix CD - no remaster needed even though the website and updated files are on hard disk. I have set up a shell file to copy config files as needed so they overwrite the original distro ones. I have a folder called knoppixmods in my hard drive that contains these mods.
You dont need to copy the apache(httpd) config file because you can start it with the -f option to point to the config file. I havent found a way to do similar with mysqld. Has anyone any clues? Also the mysql.host file needs rebuilding every time i reboot so am looking into that.

modified files list:
fstab
hosts
httpd.conf
modules.conf
my.cnf
php.ini
smb.conf

The my.cnf file sets up pointers to the database directories on hard drive plus a few odds & s**s.
httpd.conf sets up pointers to the website directory, its FQ name and a few other bits & bobs.
Both config files redirect logs to the hard drive so they can be analysed if the system falls over.

The code is as follows - including red herrings I followed. I found I didint need to chmod all originals, in fact if you make /etc 777 you cant do a sudo to get the system working. I've no doubt 'overkilled' the apache and mysql modules, but it seems to work.
Samba doesnt work properly this way, but doing it from the knoppix menu does. I'm looking into that


cd /
sudo chmod -R 777 /var
# sudo chmod -R 0440 /etc
sudo ln -s /home/knoppix/b4g
sudo cp -fs /home/knoppix/knoppixmods/hosts /etc
# sudo cp -fs /home/knoppix/knoppixmods/httpd.conf /etc/apache
sudo cp -fs /home/knoppix/knoppixmods/my.cnf /etc/mysql
sudo cp -fs /home/knoppix/knoppixmods/smb.conf /etc/samba
chmod 555 /etc/mysql/my.cnf
sudo killall apache
mysqladmin shutdown -u root -pkingkong
sudo killall mysqld
# sudo mysqladmin shutdown
# sudo chmod -R 777 /var
sudo apache restart -f /home/knoppix/knoppixmods/httpd.conf
# sudo /etc/init.d/apache start
/etc/init.d/mysql restart
# mysqld
# sudo chmod -R 777 /var

#mysql -h host -u user -p
# mysql -u root -p
/etc/init.d/samba restart