The Ubuntu 11 to 14.04 upgrade means your kernel libraries, and therefore, binaries will have to be different, including Apache and MySQL server. So, you have to install the binaries again and you can only copy text configuration files and hope that the configuration parameters still work.
For Apache, install Apache first, then:
Copy all of the text files under the
/etc/apache2 directory on the old drive to
/etc/apache2 on the new drive, preserving relative paths and replacing all duplicates:
cp -r /path/to/old/etc/apache2 /etc/apache2
Manually set the symbolic links between mods-available and mods-enabled in the new
/etc/apache2 to match those under the old
/etc/apache2. If there are modules that are renamed or use different settings and Apache complains, edit your apache2.conf, as needed. Then,
For MySQL, install MySQL server first. @vembutech's answer is good, but he left out that if you had any custom MySQL settings, e.g. for memory, thread allocation, and so forth, you do not have them in the new MySQL install. So:
Save a copy of the new /etc/mysql/my.cnf:
sudo cp /etc/mysql/my.cnf /etc/mysql/my.cnf.orig
/etc/mysql/my.cnf from the old disk to
/etc/mysql/my.cnf on the new disk:
sudo cp /path/to/old/etc/mysql/my.cnf /etc/mysql/my.cnf
Missing parameters needed by the newer MySQL can be gotten from the saved copy of my.cnf.