Audio Systems: Crackling Speakers, crackling speakers, alpine subs

Question
I have a pioneer head unit, 2 10 in alpine subs and an alpine amp. I just recently installed brand new rear speakers but still have the stock front ones. Just recently, when i turn up the volume my speakers sound like they are crackling. I took out my rear speakers because i thought something was wrong with them. I realized it was still making the sound even after i took out the new rear speakers and now the crackling is coming from the front stock speakers. I had 3 people tell me 3 different things on what it could be and i was wanting to know your opinion!  

Answer
I am no expert on car audio but there are some basic troubleshooting techniques that apply to all audio. The advise that I am going to give you should only be used to analyze the problem as far as it will take you before having to dismantle sections of the system.

1 - Is the cracking occurring with CD and radio or just one of the two? If so which?
2 - Is what you describe cracking or static?
3 - Are you able to interrupt the signal flow from the head end meaning the CD/Radio? If so you should try connecting a portable stereo or headphone and listen for the crackling.
4 - Does the crackling occur only when you turn up or down the volume or is it present at a set volume? Is the set volume at any specific level (meaning how loud is the sound). I don't expect you to tell me in db but describe it as you would in terms of speech.
5 - Did you ever notice this crackling before you installed any peripheral speakers?
6 - What kind of a load is each channel of the amplifier seeing? How many speakers per channel?
7 - I must assume that you are using an amplifier with band pass filtering meaning some kind of a crossover to drive the sub as well as the full range speakers.
8 - When you say stock, are you referring to the Pioneer and Alpine as coming with a new vehicle or was this system installed by a third party?

Lastly, you will probably get a more precise response from someone who does this work as a living. The closest I ever got to auto sound is my own vehicle. The only real difference is that the laws of sound change slightly when confined to a small footprint.