I need to setup 3000+ domain names as aliases. Currently they are setup that way on a plain linux box, but I need to move everything to new server. I do not look forward having to enter all of that manually.
The two ways to create domains through DA or by using the control panel or the API, here.
If you can't find the code you need in the API and you don't want to do it through the control panel then your options would be to contact the DA sales group and ask them about the prospects of adding the API, or learn exactly what changes the system makes when it creates an alias, and create your own script to make all those changes.