Hmm, I'd start with lifting the amp out of the combo shell then checking out push on connectors or where wires go in to connectors. Do a tap test with a pencil or something that doesn't conduct to see if you get any crackles and bangs with the amp powered up. (you might need to insert an instrument lead in to the input. I work around components to see if I can find a dry joint or anything that moves the shouldn't ha ha! I'm having a guess at a power supply issue on board, but as the spider is a DSP based amp, (I'm pretty sure of that) there's probably not a lot that can be done about the preamp side of things - which I am guessing at if the controls don't seem to make a difference (no additional noise at all when cranked up).
I worked in a school for a bit and I was absolutely gobsmacked at how students (not in my group I might add) systematically destroyed all of the guitar amplifiers over a term. Each week I would come back and find more parts missing or broken. Gutted but also very annoyed