Stock System upgrade...
 

OK ya'll I'm going to be noobing it up bigtime here, but I'm curious about why a cheap 70 dollar 5.1 surround system for my computer (specifically Logitech X 540) can sound so much better then any stock car audio I've ever heard? I understand it has access to a much stronger power source in home wiring, but damn the bass and sound is 10x better then the stock XB, to me anyway.

So next question would be what basics parts would I need to meet to match that sound quality? Seems pretty mild to me but what do I know? I'll probably eventually have around 1000 for a sound system, and fully accept I'll need to have a pro install it. Any San Diego audio shop recommendations?

The noise floor in a house is really low so you don't need as much power to get the same percieved volume as you would in a car. Another advantage is that your main speakers are aimed at you and are for the most part equidistant from you so they sound the same on the left and right.

In a car you are dealing with a high noise floor, speakers that are never equidistant from you (one side is always closer) and you can never get the speakers perfectly aimed.
Due to the nature of sitting inside a small enclosed space there are lots of nasty reflections to deal with that arrive at your ears at or greater than the volume from your speakers, so the waveform never resembles that of the original. The upside to a car system is that you can get better bass without much effort.

In a car, buying better speakers will only get you so much due to the vehicles harsh environment. This is why install and planning is so important so that you can try to address as many of these issues as possible for that home audio like sound.

^ Nailed it.

Mounting speakers in the kick panels helps to equalize path lengths, so that's a good place to start. I'd rather listen to an average speaker mounted in a good location, than a megadollar speaker in a poor location.