I'm upgrading to a new server, i've been through this process like 4-5times over the past 10yrs and its never an easy one, reconfiguring setting, installing modules, moving sites, etc. In the past I've tried both rsync and cpanels migration. no matter what method I use it still takes days to get everything moved and reconfigured. Does anyone know of a guide or have a list of sets you do...
I usually start by running the package manager full system update on the new box, then using either scp or rsync, copy all directores (including configuration files for apache and php and others I need) into a temp location on the new serve or directly into the correct location. On the new server, I take a list of the packages from the old server, edit the list removing anything that I don't need to make my web sites/databases run and then run the package installer on the new system against my file list.
Usually then comparing the different configuration files and changing to fit my new environment.
All in all maybe a day including transfer times for the files to get everything moved and back up. And that is for installing a server from scratch to having it up and running with the files and databases from another server.