Ron's got it right - if it ain't broke, don't fix it.
You want to move the SA85 card to the new PC. If memory serves, that's an old ISA bus card. Does your new PC, even if it was formatted with Win 3.1, support ISA cards, or only PCI? The clock speed will be faster - can the old card keep up (a problem with AB KT cards)?
Unfortunately, there is no certain way to know. You can contact Schneider (né Modicon) and they might tell you which PC buses have been known to work, or what to watch out for, but it's a **** shoot.
That's the hardware - now for software. If memory serves (I haven't had to think about these kinds of upgrades since the Y2K era, when everyone was ditching these kinds of systems) Win 3.1 is an 8-bit OS. Win98 is a 32-bit OS. I think Win98 has a sort of 8-bit shell that it can run 8-bit programs, but I wouldn't give you 2-bits for it.
A better option would be to upgrade the Wonderware app to the latest version, running on the latest OS (NT/Win2K) Fortunately for you, Wonderware upgrades more seamlessly than any other SCADA package. The graphics were always object-orented, the scripting language hasn't changed (at least they haven't taken anything away). So that part of it will be OK.
What might bite you is the other things the system does. Printing and datalogging technology has changed greatly since the DOS era. It used to be you just sent an ASCII string (with carriage returns - when was the last time you saw a typewriter with a carriage that had to 'return?') to the printer or a file. Now there's a ton of formatting that has to accompany it. Laser printers have replaced dot matrix, relational databases have replaced text files. You'll want to look hard at all the system does before answering whether you want to upgrade. It's amazing at some of the simple things that we used to be able to do that BillG&co took out of our hands.
Good luck!