Honestly, I would think that the problem most likely resides in the aux input panel. It is not a simple 3.5mm jack. There is a "module" for lack of a better term on the backside of that panel. I'm not sure whether it's there to reduce noise or serve some other purpose, but that panel comes off very easily. I don't know whether the module can be disassembled at all, but I would take a peek at it first. You might try hooking an ipod up to the aux input and taking a voltage reading off the pinouts from the backside of that module. I'm not sure whether the voltage would be enough to read, but if you get readings, then at least you know it's outputting a signal of some sort. Otherwise, you might want to try replacing it and see if it fixes your problem. It's probably much cheaper than replacing any other audio system component and is the likely culprit.