If you got a subwoofer control option on your hu you need to turn it down 3-4. If not setting your bass down to about -2 or -3 should do. What is happening is your subs are stronger than your amp so they are trying to **** extra power from it which is causing the amp to **** extra power through the preouts. Therefore your sub amp is robbing your components of power causing them to distort do to lack of power. Which is also the reason the one speaker cuts out completly. You component amp aint is trying to use what little power it can get to power 4 speakers but the little power its getting probably isnt enough for 2 let alone 4 so its trying to divide it equally.
You need to sell the amp you got and get a better one before your subs burn it up cuz then you wont be able to get nothin out of it. If you dont it could short your whole system then you'll have to replace most if not all of it...
^^^^^ Thats your only option. If you dont eventually those subs are going to burn up your sub amp by drawing to much power through it. And possibly burn up your head unit and component amp to by drawing extra current through the preouts to try to feed the subs and by starving the component amp which will overwork it and eventually kill it.
none of this is even remotely logical or can be explained using electrical theory. i'm not sure you actually understand how amplifiers work or how this system is even wired. i recommend the OP (and anyone else) pretty much disregard everything stated here. no offense, just trying to prevent the spread of mis-information. i do appreciate your desire to figure out the problem, but without an understanding of electronics (i'm an electrical engineer) you are getting yourself (and others) confused.
sounds like the factory Infinity amplifier is powering the factory Infinity speakers. and all of the wiring between factory amp and factory speakers is also factory. assuming no one has modified this wiring, it is not suspect. The OP bought an integration harness that allows him to feed the factory amp a signal from the aftermarket head unit. This signal can be either from RCA outputs or speaker-level outputs. the sub amp and sub have nothing to do with the problem electrically. factory amplifiers can and do fail. the actual amplification comes from STK packs that are basically an IC with 10-12 pins and each one is dedicated to a channel or pair of channels. all it takes to have a problem with a side cutting out is a slight loss of electrical continuity where the IC connects to the board. Vibrations can cause this to happen, but so can temperature or even humidity. higher frequency vibrations are much worse on electronics than low frequency vibrations - which supports your findings. Even without the sub on, heat will cause the same issue.
with some infinity systems, each speaker is powered separately - which can also explain why it's not an entire side but individual speakers. since the factory amp is getting a signal from the head unit (presumably the speaker outs so fader/balance are maintained) and because only one of the front left speakers (not both sail and door) are cutting out, the problem lies in the factory amp. if the problem was in the head unit or head unit wiring, you would lose entire sides or areas (both door and sail).
if both sail and door speaker behave identically (Cut out at the same time) then the problem could simply be in the connection behind the head unit to the integration harness. if you didn't solder/heatshrink the connections, they are always suspect. even professional crimp connections can have issues. a slight short in speaker wiring will not cause fire nor smoke. the channel simply shuts down or cuts out. it can be intermittent or stay that way until the fault is cleared - all depends on the protection circuit in the amplifier IC (the head unit and factory amp use IC amplifiers with built-in protection). the only way to solve a short is to redo wiring - not just look at it and think it's ok. if you twisted wires and taped them, that is always problematic. if you crimped, pull on both sides to verify mechanical strength. connections are usually the weakest link of a system.
voltage drop caused by the sub amp would result in a loss of all speakers as the factory amp shut down. since you don't experience that, we aren't concerned with the sub amp or sub electrically, nor will you destroy anything as described above.
yes, you can replace the factory amp with aftermarket, but you will need to deal with the crossovers for the factory speakers. it sounds like they are currently "active" and thus you will need a passive crossover for them. most Infinity speakers are 2 ohm so you need to take that into consideration when building a custom crossover. don't let this concept overwhelm you,
Parts Express has charts/tables on component values and configurations and you can build your own crossovers for around $25 per side (12dB/oct including boards). do inspect the factory speaker to look for a crossover on the tweeters (could be a simple non-polarized capacitor in series).
when adding an aftermarket amp, the wire harness adapter you got becomes useless. if you get an amp with high-level inputs you may be able to reuse factory wiring to the amp and maintain balance and fader with your head unit (since it lacks 6 channel RCA outputs).
good luck and have fun with the project. upgrading factory pieces is just inevitable and would have likely been needed even without the addition of a sub and sub amp (though it's possible it sped up the process) //content.invisioncic.com/y282845/emoticons/smile.gif.1ebc41e1811405b213edfc4622c41e27.gif