Hmpf, I'm a douche!
I forgot I still had the driver files in c:\pebuilder3110a\drivers\ -folder. I deleted them and changed the BartPE source to Windows 2003. After rebuilding I was now able to boot the server and see the hard drives.
Thank you!
And many thanks to DELL who forgot to enable RAID during the factory installations... It took a few days to get to the bottom of this, but at least I learned a great deal in the process. Hopefully I will remember at least some part of this later on.
Yet again, thank you OverFlow!