I sent an e-mail to the author of 64HDD and offered to port it to Windows. This is his reply
Nice to hear from another C64 fan from Perth - there seem not to be too many around.
On the Win32 front, the problem with 64HDD is the strict timing in multitasking environment. With CBM4Win, it is the master so its able to (mostly) control the timing of the protocol to the drives (slaves). 64HDD operates the other way around - it needs to always be a ready watching for signal edges and respond. This needs to be done with exclusive polling or high priority interrupts. Unfortunately only one interrupt pin on the LPT port.
The only way I believe to get the program working under a multi-tasking OS with some hardware to do the low level signal work. Had started something a few years back with a German friend, but "life" things have taken priority.
Hope you get your setup up and running,
So looks like I will have to run it in DOS then!