wow, forgive my sarcasm but I have to laugh a little before I help you. Ford has never made a mach 400 system and hasn't had a 6 x 9 in a mustang for almost 20 yrs..... Sorry I am a D, I am sure you mean the mach 460 system and 5 x 7 speakers but now to help you........
Did you hook up the blue wires on the pioner radio? The remote output on the radio (blue/white) needs to be connected to the amplifier turn on(blue or blue/white) on the harness side. The woofers will probably make a loud turn on pop when you turn the radio on, check the forum sticky on how to fix that.
Page 2 of my cardomain page shows how to put a deck into a mach system but it doesn't have to be that hard.
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http://www.cardomain.com/ride/2395420
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