I'll try that. I don't have physical WB 3.1 disks sadly, so will have to do it on UAE as I have the ADFs thanks to Amiga Forever. I'll post back if I get anywhere.If the caps lock is only blinking when the KA47 and SD card are connected then the chances are is that the SD card itself is not properly configured causing the lockups.
Try connecting it all back up, boot from the HD install floppy disk and start again from scratch. Much easier (and faster) than diagnosing filesystem errors.