FileMaker Server problem on Mac Mini Server - Mac Mini won't boot

I just installed a brand new Mac Mini Server today, and also FileMaker Server 11. A first-timer for both Mac OS X Server and FileMaker Server, I made an error as explained below, and right now I don't know how to get back on track with the system. It won't boot.
So, how did this happen?
At first everything was proceeding according to plan. I configured the pre-installed Mac OS X Server on the Mac Mini with users, groups and services. This was tested from clients and this seemed to work just fine. Then I installed and configured FileMaker Server. This was also tested from a client, and the example database that came with FMS was served up just fine.
The problem arose when I tried to install my existing FileMaker databases. I simply checked to see where in the file system the example database was located, and then copied my old databases to that location (I think it was Library > FileMaker Server > Data > Databases or something close to it - can't check it now...). I had the FileMaker Server Admin Console running, and hit the Refresh button hoping that this would make FileMaker Server find the databases.
This was my first error. I should have read ahead in the instructions to see that one is supposed to use an Upload Database assistant instead...
What happened when I hit refresh was that the FileMaker Server Admin Console became completely unresponsive with a spinning ball as cursor. I left it for about an hour hoping it would terminate, but gave up and tried to shut it down. It wouldn't close, so I force quit it from the Finder. Then I tried to shut down FileMaker Server, but I needed to force quit this as well. After this I thought it would be best to reboot the Mac Mini, so I shut it down, but now it won't even boot, it just stays on the screen with the spinning wheel for ever!
I have tried all the keyboard options while booting, but nothing seems to help. In safe mode, the grey progress bar just grows to about one third, then disappears and leaves the eternally spinning wheel.
The server version of the Mac Mini doesn't have an optical drive, only two internal hard drives. I tried to reinstall from scratch using the optical drive on another Mac on the network. The startup disk appeared when I tried to boot the Mac Mini holding down the option key, and after about 20 minutes or so of the spinning wheel I could actually access the discs. I started by running Disk Utility to check disk permissions. There were a lot of repairs concerning permissions and groups, especially on "Library". It said "ACL differs on Library", I don't know what this is but this was repaired. I then ran Repair Disk. The volume appeared to be OK.
When I tried to reinstall Mac OS X Server however, this failed with the message
"You can't upgrade this version of Mac OS X because a newer version is installed. Mac OS X Server couldn't be installed on this disk." I don't know how this can be, but I may have run software update earlier today.
What should I try next? Should I erase the primary HD and try to install again? Or should I install the system software on the secondary HD? Or should I just try to reboot as is in the hope that the disk permission repairs did the trick...?
Any helpful pointers would be greatly appreciated!

Hello there, I came across your post when browsing the forum for passive advice. I am in the same boat as you and am a first timer for both of these tools. I work for a company who now needs to expand its network and database capabilities. I have been assigned this task and these are the tools i have opted for. I have not yet purchased them and i am pleased to find someone who has my desired setup. Could you please advise on the simplicity of the setup and whether an advanced knowledge is required.
I want to use it in a mixed operating system environment. Is this possible?
Regards
Matthew

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