Changed the chmod 750 so that it doesn't run over all the existing instances.
That would make it horribly slow to create additional instances in an existing
installation with a lot of files.
Added variable to define the master instance, and then used that for making
links to the license file and ssl dir in the master instance. This fixed a bug
where we were checking for instance 1 for linking the license file. We cannot
make that assumption when supporting named instances.