My 2004 FJR1300 with 88000 miles had a noticeable clunk coming the driveshaft and drive line when shifting and going on/off the thottle. At first I thought it was U-joints so I replaced those but was not the problem. Noticed excessive backlash at the Middle drive gear so re-shimmed that from...
Do you have notice more the normal clunking coming from your tranny or what sounds like rear differential or U-joints? Could be your middle gear needs to be shimmed down a bit. Did that to my bike and made a big difference. My 2004 FJR1300 has 82000 miles and was getting a little loose.
