Lostbears, I have the same experience with my REF5se. I have tried the Harmonic Resolutions dampening plates and found those to prove a more noticeable improvement over the lexan cover. In answer to question above on the amp, you may try these as well. They come in different sizes, I have the small and am planning to sell those and buy a larger size.
Amplifier Enclosure Resonance
If I tap the top/side cover on my Audio Research Reference 75 SE amp, it has quite a tinny ring to it. I'm thinking that can't be best for the sound. Does anyone know of a product that I could place on top to control that resonance? It would have to be three inches or under, wide, and somewhat heat resistant.