Ok, I ran Winuae without the -disableharddrivesafetycheck option an loaded it up using the workbench install floppy. I then ran HDToolbox and made sure it said SCSI_DEVICE_NAME=uaehf.device
I was FINALLY able to get it to see my CF card. I was able to partition the disk drive, but even though it sees the full 4gb, I made two 250mb partitions (one for the workbench install which is DH0, the other for programs which is DH1), and then a 1900mb partition (DH2) and another with the rest DH3. I then rebooted workbench, and was able to see all the partitions except for DH3.
What is the largest size for a partition?