Clover won't boot if my backup OS HDD is connected

[BreBo]

Is there anything else that I might consider to try to get this working?

Your motherboard has the Marvell 88SE9172 chip with:

• 2 x SATA 6Gb/s connectors (GSATA3_5, GSATA3_6) supporting up to 2 SATA 6Gb/s devices

Try MultiBeast > Drivers > Disk > 3rd Party SATA
This will install AHCI_3rdParty_SATA.kext in /Library/Extensions