Extremely slow boot after new RAID on SBS 2000

Here's what happened - one hard drive on my Power Edge server went out. I can't replace the hard drive, it's too old. I had a new ATA with 2 hard drives to install. I copied all the old material from the RAID array to a new IDE drive. I took out the old SCSI card and 2 hard drives. Replaced the new PCI card and hard drives. On boot up, everything slowed down. Booting up took several hours! So, I removed the new hard drives and RAID card, put the old setup back in the server, but the boot up speed was not improved. Something has caused the boot up speed on the SBS 2000 server to really have problems, and I have not been able to find a solution yet. Thanks if anyone can help!