Hi,
One option that you can try if you're on v7 is using PropertiesFileBasedConfiguration tasks of wsadmin to add to your processing.
publib.boulder.ibm.com/infocenter/wasinf...
After creating the server you can extract it's properties
wsadmin>AdminTask.extractConfigProperties('-propertiesFileName ConfigProperties_server1.props -configData Server=server1 -filterMechanism NO_SUBTYPES')
Edit the resulting file and find the section "Ports Section", modify the port values and then change them in the configuration via:
wsadmin>AdminTask.applyConfigProperties('-propertiesFileName ConfigProperties_server1.props')
I also looked at using server templates for creation but that doesn't allow you to specify the ports.
Hope that helps