Captain Bugger (or do you prefer Capt. Nuts, Capt. BuggerNuts, or just "Tugger"?),
According to the on-line Yamaha parts fiche tool at Boats.net:
http://www.boats.net/parts/search/Yamaha/Motorcycle/parts.html (http://www.boats.net/parts/search/Yamaha/Motorcycle/parts.html)
...the same part-number coils are used on *BOTH* year bikes.
If you look up a part for a particular bike:
http://www.boats.net/parts/search/Yamaha/Motorcycle/1990/FJ1200A/parts.html (http://www.boats.net/parts/search/Yamaha/Motorcycle/1990/FJ1200A/parts.html)
then click on the _part number_:
http://www.boats.net/parts/search/Yamaha/Motorcycle/1990/FJ1200A/ELECTRICAL%202/parts.html (http://www.boats.net/parts/search/Yamaha/Motorcycle/1990/FJ1200A/ELECTRICAL%202/parts.html)
it'll show you the *OTHER* model bikes that part was also used on:
http://www.boats.net/parts/detail/yamaha/Y-3CV-82310-00-00.html (http://www.boats.net/parts/detail/yamaha/Y-3CV-82310-00-00.html)
Very useful tool!
Hope this helps,
Steve