A 20 year old bike with 5,000 miles? Outstanding! I think you are in for some preventative maintenance. Have a look at this thread:
This article is the result of collaboration by Andrew Shadow, CYYJ, jfheath, Max Pete, SMSW, and SupraSabre. Igofar’s list was copied from the first link listed above. Click on the attached file. This one is V.11; in the future, any changes will be noted in the title on the first page as the...
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Been hanging around here for a few years, and I cannot remember* anyone ever posting a rod knock. Whatever else might go wrong with these bikes, they got the basic engine/transmission right. I would suggest you grab a cheap Harbor Fright stethoscope and go over the engine with the fairing off to localize the noise. The clutch rattles and is noisy and that would be my first guess.
*Yes, I am getting older (most of us are, and those that are not, don't remember too well) but my memory is not that bad...yet.