As it seems with all hardware issues when I deal with them, a 10 minute job turned into more like an hour. This time the causes were:

- me figuring out how to get the drive out of the server itself
- me making a typo in the boot config for the new kernel
- me forgetting to compile the newly renamed SATA drivers in the new kernel
- me recompiling the kernel to load in the new modules
- the system taking ages to boot because all the drives had to be
filesystem checked as the last time it rebooted was 253 days ago :)

Other than those minor details we're back up and going on a modern kernel and a proper backup drive. Thanks for your patience everyone!