For proper support of big HDDs you should use the very latest version of IDEfix. See IDEfix97 on Aminet.
Also you should not mix OS3.9's new scsi.device and IDEfix' one. So either run IDEfix and change SetPatch to SetPatch SKIPROMUPDATE "scsi.device" or don't run IDEfix and run SetPatch without any additional parameters.
Finally you should make IDEfix reset resident. Run C:LoadIDE instead of C:IDEfix and make sure that SetPatch resets at its first call.
Bye,
Thomas