they should be tha same thickness.... look inside at magnet size.. a 40 amp system will work with either tha red flex plate like tha one that came on yours or tha later model black cast... sounds more like what faz thinks only other way around maybe... 16 amp stator and 40 amp flywheel maybe?... they did make both tha 16 and 40 amp systems in '89....
or tha reg/rec could be tha culprit.....