What copy method are you using? Did you try the robocopy syntax? If so, maybe try adding /r:2 to the end. This will limit the retries to twice on failure.
I'm running Windows Server 2012 and 2012R2 and I don't have any problem copying files that are in use. On the other hand, you don't need the logs. You're probably going to delete them anyway. Maybe you should tweak your copy script to just exclude them.
I have SQL fully installed on both the production and test database servers. To copy the database over I'm simply making a backup of the database on the production system, physically copying the file to the test system, then restoring the database from the backup. If you've never had a Windchill database in the test system before, you will also need to create the proper SQL login for the Windchill database user.
I actually performed a clean installation of Windchill on the entire test environment and then later did the clone. This had the benefit of getting the proper shortcuts created for the Windchill shell, getting the database server properly configured, etc. Probably worth doing...