I want to interface an arduino uno to an ISA port device, and output to the USB port, or Ethernet if possible.
Anything is possible with enough time and money, but I wouldn't expect your Windows 98 ISA drivers to work when your ISA device is presented as a USB device. Doesn't this mean you would need to write your own device drivers for it? I have no idea how complex that would be or even whether it would be feasible within an Arduino. I would have thought your best bet would be to get an embedded PC with an ISA bus running some flavour of Windows and see if you can get the drivers working.
What is going to consume the data retrieved from the spectrometer? Does this already exist, or is it something you intend to create? If it already exists, that's another compatibility restriction you will need to work within. If whatever-it-is would run on the embedded PC using the existing drivers, that might not be a problem. But if this is going to be remote (you mentioned Ethernet) then you've got a whole new set of drivers to design and implement if you want this remote spectrometer to be presented as if it was a local device.