While you have the bike in pieces, greasing the rear suspension linkages is advised. At the factory they use about a teaspoon full of grease spread among all the bearings. A long term fix is to put in grease nipples but not essential if you don't mind pulling it all apart now and then.
There are a couple of holes in the lower frame where the long bolt goes through (the bolt behind the plastic caps adjacent to the footrests). I'm not sure of the intended purpose for these holes but they sure do let water in, and once this bolt corrodes into place it can be a hell of a job getting it out.
refers to the Gen 1 bikes but it's pretty much the same with the Gen 2s
Pete (in New Zealand, watching your ride with interest and envy)