David,
For about $50 in coatings and materials, you can quiet your whole boat down, using these rod trays as harmonic dampeners.
You need as much metal-to-metal contact on the gunnels and then the right stuff (only on the trays). It would serve as double duty to keep your rigs safe as well as quieting the boat down considerably. Basically, rubber undercoating on the inside of the trays and Dynamat on the underside. It won't eat up your interior volume of the trays. Not hard to do, but I think this is your best solution.
Bottom line, things won't clank, they'll thud- across the whole boat. Drop a 3/4 oz spinnerbait on the hull and it will just donk. The principle is "sound" and it works. Your trays are, in effect, harmonic dampeners for the rest of the boat. You can test it yourself without commitment with common household materials.
PM me or just call 500-9578.
-Jonathan