What about a USB to parallel port adapter? Not sure if it'd do the job but I'd try Win2K, since it has much larger memory support and is far more stable than 9x.
As for bypassing or reverse engineering, you might see if any of the filesharing sites have a disabled version of the app, or contact the company and see if they can do anything for you, they might have a patch themselves. There might also be some sort of hacker tutorials out there that give an example of how to edit an app to remove the hardware check.
But OP isn't deciding on using any Windows 9x system. Both Windows 7 and XP support parallel ports when done right, but he might have better luck with Windows XP.