I installed an after market subwoofer and amp connected to the factory radio. It worked fine for a couple weeks, then the sound from all speakers stopped with the radio display still on. I checked fuses the next day, all were in tact, so I turned the radio on and all speakers played normally. I assumed a fuse had a bad connection and by pulling them, I fixed it. It worked fine for 2 days and did the same thing again.

I am guessing it has to do with the radio overheating and some type of protection in the radio causing the issue? Has anyone had this issue before?

 

I suspect a slight short in the wiring you intercepted. You need to ensure that all connections are securely connected and fully insulated from any other wire and from any conductive service.