Sorry, I forgot to come back to report that everything worked perfectly! Thanks for all the help. That W98 machine is still going strong and with 2 serial ports connected, plus the graphics card outputting at high resolution (found the correct drivers by miracle).

Congrats on getting it working. If the software is that critical, it might make sense to test it out in a Win95/98 VM running on a more modern system.

Most VM software I've used lets you redirect serial ports to physical host ports. Then you can have easy backups, and can quickly more to new hardware if you ever need to.

I agree, VMs are so convenient. Though messing with old hardware has this nostalgic feeling, and I learned a lot while getting it to work. I saw it as a challenge.