Hi, Please have a look at the following thread. Is this what you are looking for?

https://jazz.net/forum/questions/81110/how-do-i-upgrade-from-clm-3013-to-clm-40

Best regards,
-Vlad

First of all the Windows 7 32-bit or 64-bit environments are not officially supported so this must be kept in mind in case you have any issues with this development/test environment. You method of moving the product from one app server environment to another is exactly the suggested steps.  Although there is no particular topic in the Information Center that calls out the steps in how to move from one app server to another, you got it right.  By moving the configuration files and the index files from the old server to the new server you can move app server environments.  You should not go through setup but rather rely on the already setup configuration and friends files established when setting up on the old app server.

This is the expected process to be used in your production environment move as well.  Please note that in moving from one app server to another, you must either maintain the same established reverse proxy machine and its DNS server name as that of the public URLs used to access the apps on the app server OR you must rename or alias the new app server to the server name contained in the public URL that was used to access the applications on the old app server before the move.  This may involve a DNS update and possibly even decommissioning or renaming the old server since it can no longer use the server name from the public URLs.

The process of moving from one app server to another is described as part of the server rename user scenario of moving a copy of the production environment and setting up a staging environment.  It describes what configuration files and index files should be copied over as well as how to establish a copy of the production database to "seed" a staging (or dev or test) environment with a copy of production data.  While this server rename feature is only present in the v4.0 product, the steps to transfer the applications from one app server environment to another are valid for your purposes and should equally apply to older product versions as well.

In terms of migrating from v3.0.1 to v4.0, there are numerous resources to help you with this process.  The Information Center has a topic describing this with all the detailed steps that you need.  As always the v4.0 product will be a side by side install with the working v3.0.1 product on the same server.  The steps are pretty easy to follow in the Information Center.  There is also a jazz.net article on the migration process that covers considerations such as staged migration of the different CLM applications as well as data warehouse and RRDI upgrade considerations.  The order in which integrated applications are migrated is important so reading through the planning steps and making choices based on your configuration is worth taking your time to walk through.

This migration article is found at the following URL:  https://jazz.net/library/article/819