I don't see how putting drives on a rotation schedule will protect the motherboard. You need a case with good ventilation, preferably a case that has removable dust screens and two or more case fans (hopefully one blows across the drive cage). If the case doesn't have a dust screens, you may want to peek inside the case every month (more or less depending on how dusty an environment it's in). Use an air can to get rid of any excess dust as it helps trap in heat. Removable dust screens are nice - sort of like a lint filter on a dryer.
Also, like other suggested, RAID, other than raid 0, can be of big help. Using RAID 1 or RAID 5, the system can still run with a single drive failure. RAID 6 can be hard to come by, but two drives can fail and the system will still run. Just remember, RAID only protects you from a failed drive, not accidental deletion, viruses, or malware, so you'll still need a good backup policy in place.