The files in the "Do not overwrite" section of the white paper do not exist yet because the newly created user has not been configured yet in Peg. They will be created when you configure the new user. I do not understand why they were not in the mailbox directory that you copied unless you were running with different Home and New mailbox locations.
Best thing to do is to configure the new user then copy into the new mailbox directory only files as listed in the white paper. If the copied mailbox directory contains a pmail.ini file consider using it as a guide during configuration.
The ONLY condition under which it is ok to copy an entire mailbox directory from one machine to another is if the paths to both the executables and the mailbox directories is identical on both machines. Otherwise the invalid paths in the configuration files make Peg non-functional and difficult to troubleshoot. I also believe that if an installation has been through multiple upgrades then at some point it is worth starting fresh with a clean install and just copying over data. This insures clean config files and no "ghosts" from previous installs.