Just thought i would add to this thread rather than creating my own... Awesome write up and detailed pics.
Mine is a 2004 roadster, the previous owner had done a horible job adding two amps to power the 10 stock speakers
so I decided to re do everything including all wiring.
here is the previous owners wiring...
Most of my system is by Alpine, a brand i have trusted for a long time.
Added the Bluetooth and the little red box is to adapt the steering wheel controls.
The head unit is really made for ipod, i had the original in my old car and loved it. The mids are 4" (100cm).

Not pictured is the PDX-F4 amp that i'm using to power the 6.5" components and the JL 6w3v3 Subs, the 4 mids are powered by the deck.
Almost every panel in the car taken off, just shy of 17 hours of my time to install, paid a shop to do the steering wheel controls, front kick panel speakes
with tweeters located in stock locations and to wire up the bluetooth, 3 hours. Almost a full 100 feet of wire went into this install to get to all the speakers...

Started raining so i had to improvise, i should have done this at my condo in the underground parking instead.
Note the awesome random license plate i happened to get when i registered the car!
The original owner cut the factory harness so i had to solder in the new one in the dash, kind of a pain.
head unit lights up blue or red. kind of matches the interior lighting.
for the 4" speakers in the back, these alpines fit great, two top screws in the factory holes and the two bottom tabs drilled into the cars metal with self taping screws.
The door speakers i used two original mouting holes then cut up a full bracket that came with the speaker to make a little holder for the third location.
Seen on the left and cut the 2 tabs from the speaker. They are all sealed with 2 way foam tape.

The original speaker grills will need a bit of tweaking for bothe the front and rears... i will be bumping them out since the tweeters touch the grills if installed rightr now.
The subs were mounted on the factory metal plates, 3 of the 8 screws and bolts for this sub could not be installed because of clearance.

Always use proper connectors!

I'm very pleased with the result. parts and the 3 hours labour came to less than $2000 CND.