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UPDATE!
I've done almost a complete disassemble and reassemble of the major bolts, panel screws, and some of the rubber bushings that hold the various plastics together. On the swingarm bolt and the two engine mounts, I put rubber washers on the side of the bolt head in order to take out some of the vibration as well as lock washers on the side of the nut. I also took the suggestion of putting some rubber washers between the metal mounts of the frame and the panels (so they're hidden from view) - after reassembly, whatever was causing the clicking has vanished - and I'm pleased to report that the bike is smooth as butter now.
I believe the original issue lie within the engine mounts - I noticed that the nut on the engine mount that is behind the rear set was not as tight as it should have been, and was spinning a little when I revved the engine. I put a lock washer under the nut and re-tightened it, and now it doesn't do that anymore.
Learn from my example - tighten your nuts, people!
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