How to stop Setup Assistant from showing up on every restart on Mac Mini with OS X Mavericks?
If Setup Assistant is running then the boot process almost certainly found no copy of  /var/db/.AppleSetupDone

Try sudo touch /var/db/.AppleSetupDone in Terminal then reboot.

If you are having trouble after that with strange parts of the install process staying around then you may have some widespread permission problems. Use Disk Utility to verify and then fix permissions on the volume and see how much that will fix after another reboot. You may find the problems still there on the first reboot after fixing them - it's the second that will tell.

I doubt if the Server app is causing anything as it really is just an application that provides a GUI for setting up some stuff already on your Mac.