Migrate 14.2 to 5.0 new server

instead of upgrading my controller to 5.0 I want to build a new server and migrate the controller to the new server. Running mysql with one slave

Any insight appreciated

I would start with building the 5.0 server, make sure firewall settings and (if in use) web proxy are configured identically. Then copy your OpenNebula folders (/var/lib/one and /etc/one) to the new 5.0 server, find and fix any differences in conf files. (warning, when starting opennebula daemons on your 5.0 server to test, make sure it cannot reach your live hypervisors or mysql DB, still controlled and in use by 4.12 !)
Then make a mysql dump on your 4.12 server, transport it over to 5.0 and do the onedb upgrade as mentioned here:
(In your case, also look at the remarks about mysql slaves there)

If all is fine on your new 5.0 server, turn the 4.12 server off, (make sure 5.0 server can reach the hypervisors now) and see if one5.0 can monitor all hosts and vm in /var/log/one/oned.log

If your not changing/upgrading the underlying OS of your one controller, you might as well consider working with a backup of the 4.12 server on your new server and just follow the update steps from the docs ?
The only thing I am not sure of, if your one5.0 will be able to properly recognize all your running VMs, I never tried it this way. Users/groups/templates etc should work without a problem.
Hope this is helpful, good luck!

Thanks, because I am using gentoo and installed the first one manually I wanted to try the package gentoo has now. hence thinking a migration to new controller instead of up grade