ORIGINAL: mikesrt4

i recently purchased a 2006 GT with the shaker 1000 system. I want to remove the entire factory system and put in aftermarket head unit door speakers, amps and subs. mt question is this....how hard is this to do? I have bben told that the factory amps cannot be removed because they control other things in the car and that to remove it is a wiring nightmare. I know a decent bit about car systems, I have been competing in sound shows for about 10 years, but I am new to ford products and also new to cars that have factory "sound systems" like the shaker 1000. I saw online that to replace the head unit there is a special wiring harness that has a plug with 2 rca's??? What is that for? Any help anyone could give me or point me in the right direction would be greatly appreciated.
thanks in advance