You could create an advanced search for all unstored documents (Template Item equals Document and Document Size does not exist). After selecting the first search result, Ctrl+M, down arrow could be used to store each one, or possibly use a macro tool to automate this part:
http://members.ij.net/anthonymathews/MacroMaker.htm
http://www.autohotkey.com/
http://powerpro.webeddie.com/
http://www.hiddensoft.com/autoit3/
http://www.macros.com/
http://www.mjtnet.com/macro_scheduler.htm
http://www.tethyssolutions.com/product.htm