Need help with wiring new door speakers

Hi I have a 2008 Tacoma DC with the JBL sound system and im replacing the door speakers with Polk MM series components in the front and coax in the rear, the speakers will be wired into an alpine 4 channel amp. I ran all new 14ga wires through the doors to the amp and I am using a LOC attached to the rear driver door speaker for my rca's to the amp. The speakers sound likt crap and i am getting a ton of static when the stereo volume is all the way down all i hear is static and its loud enough to annoy the crap out of me! Where am i going wrong here? i checked my loc connections today and made sure the polarities were correct and everything seems to be fine there not sure why i am having this problem. My front components do not seem to be functioning properly either the voice is coming more from the mid base than the tweeters. I have the JBL sound system and am wondering if that has something to do with why im having so much trouble. Thanks for any help im not new to wiring but im no expert either so any info would help a ton!

update

Ok so I think i know the problem, I need to bypass the factory amp but im not sure how, when I tap into the rear door speaker for the LOC it is being amplified by the factory amp, i am replacing everything in the truck except for head unit, i have new door speakers a 4 channel amp to power them, new subs and an amp to power them, i just want to by pass the factory amp and sub how do i do this???? there is three connections into the factory amp, ones for the sub ones the speaker wire input from the HU and the other is the outgoing wires to the speakers. when i unplug any of the above the whole system doesn't work? FU** ive never had such a headache trying to install some speakers!

 

The new speakers will are currently wired to an alpine 4 channel and ya the crossovers are wired correctly

 

its not the gain its something with the factory amp and sub interfering read the update i just posted above