Fresh install of OS X Server but keeping data

Hi,
I run a family server (Web, e-mail, VPN) from an old MacBook Pro laptop and due to a fair amount of odd errors now appearing in the logs, I'd like to re-install Yosemite, and then OS X Server back on top so I have a fresh configuration, but I want to keep the data, such as user accounts, mail data etc.
Everything is backed up twice using TimeMachine, once to a NAS and also to a local USB, and I also have a Carbon Copy Cloner bootable image on the USB Drive too, so I'm covered on the backup side. I also have a bootable Yosemite USB thumb-drive I can use for the install.
What would be the recommended approach to doing this please?

Starting up into Safe Mode does three things to simplify the startup and operation of your computer:
* It forces a directory check of the startup volume.
* It loads only required kernel extensions (some of the items in /System/Library/Extensions).
* In Mac OS X 10.3.9 or earlier, it runs only Apple-installed startup items (some of the items in /Library/StartupItems and /System/Library/StartupItems - and different than login items).
* Mac OS X 10.4 Tiger only: It disables all fonts other than those in /System/Library/Fonts .
* Mac OS X 10.4 Tiger only: It moves to the Trash all font caches normally stored in /Library/Caches/com.apple.ATS/(uid)/ , where (uid) is a user ID number such as 501.
* Mac OS X 10.4 Tiger only: It disables all startup items and any Login Items.
Since it works in safe mode, one of these has to apply. You can also try to "zero" the hard drive and then install. I've had an external HDD, where I had to do that, before the install would take.
I hope this helps...

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