Clone the drive using something like Clonezilla or Acronis True Image and install it in the machine, and everything should boot up as it was. I've lost count of the amount of times I've cloned an OS drive. There's no need to do a clean install.
And your machine isn't necessarily going to get "confused" with multiple OS's on multiple drives. Just specify which drive you want the machine to boot from in your BIOS. I've often had Linux and Windows on different hard drives for instance.
Although I'd probably format your mechanical drive just to get rid of Windows on the MBR.