Thank you for your post. I will keep this thread and delete other duplicates then.
The ultimate goal will be to create a new AGENT.EXE thats branded and points to our private server.
As for your question, you need to specify your custom server address and port in the last step of the configuration process where you are presented with the Host settings dialog. For that dialog to appear in the step 4 you must select "Pre-configure host settings":
Then in the Host settings dialog click Settings for Host -> Internet ID connection settings -> Advanced -> Select ID server. There'll be a window where you can enter your server's address:
Then close all the dialogs and the configuration process will finish.
when i tested this i had access violations all over the place (but the server and host / agent) are all on 1 PC for testing.
Make sure that if you use the beta version, you use it for all modules. For example, when configuring your agent file feed the beta Host installer to the MSI Configurator, not the stable Host version file. If the errors persist, let us know the error text.