It looks like you have a similar issue to @powermapler who had problems dual booting OSX and legacy (MBR) Windows (installed on separate drives) with Clover.
Try @dmazar's suggestion from post#5268 in the Clover General Discussion Thread (BIOS set to boot in both UEFI and legacy mode)
- set Clover option as first one in boot order in UEFI/BIOS screen
- set your legacy windows drive as second one in boot order in UEFI/BIOS screen
- set Boot/Legacy=LegacyBiosDefault in Clover's config.plist
And then selecting any legacy entry in your Clover main menu should boot your legacy windows