I assume that you bough the 5SE used. Did you contact the previous owner and ask him if he had the same issues? There will always be a bit of tube rush noise coming from speakers, but nothing should be heard from the listening position.
You think the plastic top would be cooler. I'm not shure, Anybody else got a theory?An aluminum top will cool will dissipate the internal heat MUCH better than a plastic top. All you need to do is look up the thermal conductivity coefficient of the material use. Plastic acts more like an insulator whereas metal will act more like a heat sink. If you want to increase the cooling capability of an item, build it out of copper
Did the shipping box show signs of obvious damage? Did you take pictures of the damage before opening the package? Did you report the damage to the courier company ASAP? If the answers are no to the previous questions, I’m afraid your claim will be denied. Right now, you think that damage occurred during shipping but no physical damage can be seen. Hopefully, it will be an easy and quick fix.