Is it possible that you do not have the original engine or frame? The bikes before 2000 or 2001 had engines and frames that used a smaller diameter swing arm axle. I also heard the bottom engine mount was relocated after 2006.
I put a 2004 engine in a 2000 frame one time and needed to machine some aluminum inserts to put into the engine case to take up the gap for the smaller swingarm pivot shaft. I found that a Maglite AA flash had a correct interior diameter for the shaft but the outside needed to have a little material removed to fit in the cases.
I guess it is also possible that if the bike was ridden with a loose swing arm shaft that it could wear the engine cases and make them a loose.
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