just pull my factory stereo out of the dash...is there supposed to be 2 harnesses that plug in to the back of the HU as i see 2 places. 1 big and 1 small plug hole
My stereo only has the one big plug. could the other spot on the HU be for the amp?

 

You shouldn't have highs in your front door speakers if it is stock infinity system....also if there is another speaker that is not pulling any/all the power it is suppose to it gets added to other speakers....or your factory amp is shot! in the long run it is going to be easiest to put an aftermarket system in. I have been going through the same thing...turns out it was a back door speaker that somehow wasn't hooked up and caused me to blow first my pass side speaker, then I order a new 6X9 and unhooked blown speaker....then playing talk radio caused me to blow driver side 6X9! long story short check ALL speakers as so you don't blow them....$70 lesson for me!