We developed a workqround that mostly works. Essentially, Build a model user that is exactly as you want it then developed a MS-SQL script and MS-SQL-trigger so that when a new user is created, it pulls the settings from my model user. Not quite what I need but working better than nothing for now.
Once your model user is created you can setup the way you want them in the webclient, or in the swl table for the user that contains an XML column. Once you go in, you can configure the true or false configs. Kind of complex so be carefull.
Make sure you have good SQL backups before attempting this.
WHen creating a user, their default toolbar is preset and user may change manually. I can find the table where the settings are held.
I am however looking to find the master location where the settings are pulled from, ie, when a new user is created, it pulls the default settign from a master location.
for example: overlay1 by default is set to true and overlay 2-5 are all set to false so their icons do not display.
Where is the master pull location so I can set layers 1-5 to on or change the default annotation list.