I was very happy to discover a comment on the setup of my Intel D945GSEJT home server today. I am glad to hear that my post helped you, Jules.
The home server works very well. I have learned a lot in the few days that the system has been running, and I felt it was time to share some of the knowledge I have gathered so far.
My choice of building the system in a fanless case with a built-in power supply was not the best. A power supply inevitably produces some heat, and with the whole setup being fanless, the harddrives reported temperatures close to 60 degrees Celcius. The specifications of the drives said that this was slightly above the upper safe temperature limit for operation. I changed to an external 12VDC adapter, and got the temperature of the harddrives down to about 40 degrees Celcius, which is perfectly acceptable.
The D945GSEJT board offers two power connectors, a 12VDC connector on the back panel, and a 4-pin 12V ATX internal connector. The Technical Product Specification of the board says that the 12VDC connector is "preferred", but does not in any way explain why that would be so, which is very strange. Connecting a mini-ITX power supply (with one 4-pin connector and one 20-pin connector) requires you to short two pins on the 20-pin connector, since this is the signal that the motherboard normally gives to the power supply to make it start and deliver the correct voltages on all pins. This is not anything I recommend in any way, but it was what I had to do to be able to use the built-in power supply of my mini-ITX case. I suspect that Intel had the idea that you would use some special power supply which is always on and only has the 4-pin connector, but I have not found any such supplies. My case gave me small electrical shocks using the internal power supply, which might have been caused by my unorthodox solution, but it might just have been the power supply that was dodgy. I am glad I switched to the external power supply, which has none of these worries.
Getting acquainted with mdadm for managing the RAID, and smartmontools for monitoring hard drive health was an essential first step in learning to administer my new home server. It turned out that one of my hard drives had a bad sector, and I got to apply this knowledge almost immediately. Emails from smartd started pouring in, telling me about the problem on the drive. The selftests that I had scheduled for the hard drives had fortunately located the error to a sector which was towards the end of the drive, which was probably not occupied by any data. The solution I ended up using was hdrecover, an extremely simple (293 lines of C code) program that tests the readability of each sector on a drive. If an unreadable sector is found, the program writes some data to it, forcing the drive to mark the sector as bad, an relocate it. In my case, being fairly certain that the defective sector was not occupied by any file, this was a solution as good as any. If you want to locate the file that occupies a certain sector, this can be a bit tricky. I found a howto on this subject, but I am not sure how I would get it to work in my case, with partitions on an encrypted LVM partition.