I used diskpart to clean the MBR off the card.
On WinUAE with Classic Workbench, I replaced the SCSI.device, renamed the SCSI device name to uaehf.device and enable Smart File Format. I made the first partition below 600mb then made the other partitions and set them all up for SFS and deleted FFS. Then I formatted using SFSformat. Finally, I copied the system files of Classic workbench over to the first partition of the card.
Do I need to snip a pin somewhere. I've seen that mentioned.
Also, I heard CF cards were pretty finnicky.