If you are not concerned about saving the data it will be much easier to start with blank drives.
Buffalo provides a recovery disk image for this model you can get along with the firmware updater on the support page. You should be able to perform a fresh install using that and the firmware updater in "debug" mode.
The process is basically the same as this, only you use the recovery disk to get to EM mode and then proceed from there:
https://buffalonas.miraheze.org/wiki/Restoring_Stock_Firmware_without_TFTP For some reason these devices don't like to install the firmware unless all drive bays are filled. Some also incorrectly see 2-bay devices as 4-bay devices which can further complicate things in some cases. The guide I linked above includes a method for installing to 2 drives if you run into that issue.