Well, stock setup sucks! So I am thinking about upgrading speakers and amps but keep the stock HU.
Here are some questions:

1. Do you guys run new or use stock wiring for speakers? How hard is to run new wiring?
2. How big of a pain in the ass is fitting 6 1/2's into front and rear doors?
3. Does aftermarket setup with stock HU sound good or do I need to hook up a line output converter?

Things I have:
6 1/2 inch Diamond component speakers
6x9 Diamond speakers
2 Sony amps with custom rack
2 12 inch MMATS subs + custom enclosure
AudioControl LC6 line output converter

TIA

screws and reach under carpets...

they will still require some adapting depending on the speaker. 6.5" are hard to fit.

I have an account up in Washington that remolded the entire front door panel to fit the MB Quart signature series 6.5"

It sounded good, but looked akward.