I don't quite understand what you're asking. You want to change the rear wheel so that you can run a smaller rear tyre?? Couldn't you just put a smaller tyre on your bike's rim as it is? OR do you want another wheel so you can swap it for road use?
The wheels are totally different, and will not fit due to the '88 having a drum brake hub and the 89-2006 having a disk setup. you could possibly use a rear wheel from the earlier disk brake models, although I cannot guarantee that.