The '87 and '88 axle housing is different from the '89 and up. It switches from a four bolt to a two bolt set-up and the way it is bolted to the swing arm is different also. On the '87-'88, the housing brackets are on the outside of the swing arm brackets. On the '89 and up, the housing brackets are on the inside of the swing arm brackets.
Measure the bracket dimensions on the two swing arms and make sure they are the same. If not, you may have to shim it with spacers. I can tell you that an '05 swing arm did not work with an '88 carrier (a buddy cracked the swing arm on his '88 banshee and had to use the '05 carrier with the '05 swing arm he bought). I will never understand why Yamaha stuck with that design for twenty years , just like the stupid design Suzuki used on some of the Quadracers (that stupid sliding box , I hated that, too).
This may have nothing to do with the price of eggs and it may all bolt-up just fine, but it is something to look at.