The documentation is lacking the following instructions for running the initialize.sh script when the database is located on a remote server. For example, we created a MySQL database on a different server than where we installed manifoldCF. When executing the initialze.sh script, the database was created, as well as the user; however, the user was created with client access of "localhost" by default. When the script got to the "creating tables" phase as the user, instead of the admin user, it received an "access denied". After looking through the code, I saw that the following setting should be set in properties.xml:
<property name="org.apache.manifoldcf.mysql.client" value="%"/>
The % sign indicates that the user can login to the mysql host from anywhere. I could have put the ip address of the server where I am running manifoldCF as well, but we have no particular security concerns in our dev environment.
After setting this, the script ran successfully.