Printing to the network potentially kills two birds with one stone, getting the file off the scope onto the network and handling PDF conversion, but there are of course many ways to skin this cat. I assume you can set up such a print server using Windows too, I'm just not a Windows guy.
Well as I mentioned, I have a Raspberry Pi sitting around and that runs Linux. I don't know anything about servers or anything more in Linux that a GUI and basic commands though.
As for the comments about installing Win10(!?), I surely hope you're joking because Win98-era hardware is probably going to already be too slow for XP, and it being a scope means the DOS-based Win9x could be allowing scope software access to the hardware directly.
If you read further back, you'll see I stated that in order to upgrade the OS, the motherboard needs to be replaced. This scope is old, and, in my opinion, has many un-repairable points of failure due to obsolete components such as the hybrid chips. I can spend time and money trying to update the Windows portion of the scope, and eventually a component can fail that would make the scope unusable. In the end, I'd be stuck with a "computer" that I can't really use elsewhere.
As for the cost, not that a new motherboard is expensive, but I feel it's a waste of an expense based on what I stated above (and this assumes I can even find the scope software which seems obsolete too - I'm uncertain how others have done it but they have registered copies of Win10 and are understandably unwilling to provide an image).
Also, as far as I can tell, Windows plays a very small role in the the scope. Windows is there to automatically launch the scope software and handle providing drivers for hardware. The scope is outdated not because it's slow, but because it's Win98 based. I'm trying to find a printing solution that isn't a lengthy process because I may decide to print several waveforms while measuring a circuit, and a process that doesn't result in having to find another solution in a year because this one is outdated already.
I'm uncertain if a Raspberry Pi is the best solution because I would need to connect it to the scope each time, and then connect to the Pi to extract the files, however, I feel unless I find a piece of software that works on a barebones Win98 OS that prints to PDF successfully, this may be the only other option.