Hissing isn't a result of a ground loop. THe issue you are most likely having is an issue with input sensitivity matching on the factory amplifier. The output of the Pioneer is probably much greater than the factory system.

Bypass the amplifier and I can almost guarantee it that the hissing will go away.

 

Pretty much what I was going to say but better.

Aftermarket HU's and Stock Amps very rarely play nicely together. I believe the output on the 4400 is 4.5v and the input on the factory amp is probably 2-2.5v

 

I have found that, on most cars, it is usually faster to run new wires from the deck to the speakers than to find and mess around with the factory amp.

 

I find that in all cars its a lot easier just to run speaker wire from the radio to the outputs of the amplifier. No need to worry about the possibility of molex plugs, etc.

Factory wiring is more than sufficient to run deck power.

 

How do I bypass the factory amp? Isn't removing the stock radio disconnecting the factory amp?

If I bypass factory amp, do I still use the stock harness for connections?

Is there a way to reduce the output of 4400? Maybe add a resistor?