With the ford amplified systems the factory amp turns on with a 5v signal not a 12v signal that after market radios use. If you don't use it you will hear a loud "POP" from your speakers when you turn the car on and off. It's annoying but not a big deal.
As in distorted sound? A after market radio dose have more power than the factory radio and running that audio through a second amp can distort it. Try turning your loudness settings off. You may give some thought to bypassing the amp all together.
It could also be possible that you wired your speakers backwards, that can cause issues.
Or it could be that with actual power you are now finding out that your factory speakers suck.
Just for some clarification is it only AM/FM or only on CD or only on AUX that your getting poor quality or is it across the board?
Assuming all your wiring is solid and nothing is hooked up wrong and the factory radio sounded good you aftermarket radio could be bad or more likely you are over powering your factory amp and it is causing distortion. I would try bypassing the amp an see how that sounds.
That's a solid deck. I doubt it's bad. I think out of the hundreds of pioneer decks I've installed only 1 has been bad out of the box.
So there are two ways to do it. You can run all new speaker wire to the factory speakers from the back of the head unit or you can cut the speaker wires going into the amp and attach them to the corresponding speaker wires coming out of the amp.
The latter is the easier. All you need is a pin out for your amp.
I. Did is a while ago and can't completely remember! But I know I used a write up by a guy to install. he said nothing about the converter in his write up but I just hooked it up using the instructions that came with the converter and the write up. If you can take a picture of the instructions I can probably figure it out.