Whenever you open or close the trunk you are changing the electrical characteristics due to inadequate grounding of the lid. Install a ground wire from the trunk lid to the chassis. Also ground the amps and any other metallic part of the sound system.
And don't asume the threads of a sheet metal screw are an adequate ground. Use grounding washers and grind the paint off where the washers sit, then prime and paint over the tightened screws.
This makes it sound like its the actual fix lol is it normal for cobras to do this with the stock mach 460 or did i just get a funny one? I'm kinda picky and would probably not like to screw holes in my cobra or even sand down the paint anywhere in it unless i had some feedback from someone who has had the issue with the car and did what you stated and got rid of the problem.Reason is if i drill holes and grind off paint and don't get rid of the ground noise its gonna make me very unhappy and with extra holes in my car hahahah. If possible can you show me an example of what i should do properly maybe a picture or quick vid would help.