well, the number one problem is all that mismatched equipment. trust me, jvc headunits don't like to play nice with other brands.
Have you checked the grounds throughout the rest of the system? off the radio, are the speaker wires frayed and touching someplace? Is there a bad connection some place that could be sending a surge through the system? Those will be the first things you should be positive about.
I have a similar problem, similar equipment, and for me it's the processing units inside the head unit are trying to crap out. everything except the amp cuts for less than a second then resumes playing like nothing happens. Everything works flawlessly except for that one problem that just randomly pops up. What sony amp do you have? I'm pretty sure most sonys have the green LED status light on all the time, it's when the orange or second light kicks on that you have problems. I've frequently tripped the thermal protection on mine, lol
My best advice, double check all the connections all around. it's possible a loose ground is the culprit. If that leaves equipment error, you can try to replace the headunit and try to get more compatible brands(i.e. sony amp and sony HU, jvc amp/hu, etc)
Last edited by Gearhead31; 09-27-2013 at 05:41 PM..