I was wondering if it's even necessary. My 2000 GS has a slight bit of rust here and there, The chain is brown, but doesn't look eaten up or anything. Would it be a waste to replace the chain and sprocket? Is there any type of upgrade I could replace them with?

If there are upgrade options, does anyone know part #'s or sizes? I got a lot of bike shoppin to do today  But 'tis a labor of joy 

Clean the chain.  I suggest kerosene from Orchard Supply or Home Depot, and a soft bristle toothbrush.