try posting in the after effects expressions forum, i think you'll get more responses over there.
you can also checkout
aenhancers.com to see if any one has something similar, or even put in a request for that script.
i think you may actually need a visual basic (pc) or apple script to run that will open ae and have it import a project file (your template). i believe this is true due to the requirement to open the application (an os function), then import a project (an ae function). if you use a java script, i think you may need to run it from after effects via file>scripts>run script, and at that point you could have just imported the project manually...
i'm not an expert on scripting in ae, but that's my understanding of a limitation with java scripting in ae...
if there is an easier way, i hope somebody chimes in...
of course, you could just open the template project file (from a shortcut on the desktop or something), then do a 'save as' to rename it so you don't modify your template... but i think that maybe what you are trying to avoid.
Kevin Camp
Senior Designer
KCPQ, KMYQ & KRCW