are there ways to run my Scout server application under a special account (I am using Windows / Tomcat). I need this because I need the server application to be able to access certain directories that are restricted for most users.
If you have a Tomcat default installation on Windows, Tomcat is registered as a Windows Service. In the Service properties you can specify the account under which the service is running. By default this is the local system account, but you can change it to any user you like.
Open the Windows Services Console (type "services" in the start menu search field), you should see a service listed as "Apache Tomcat 7" or similar.
Open the Service properties (right click -> Properties), switch to Tab "Log On". Change the logon user from local system account to a specific user and provide username and password.
Alternatively you can access the Service properties via the tomcat7w.exe (note the w in the file name!) from the Tomcat installation folder.