Wow, I did my stereo upgrade the exact same time you did! Early on, I know that one of my tweeters (drivers side) was not working, but otherwise the system sounded okay, weak on bass, but not terrible. My biggest issue was not being able to connect my iPhone.
I started off replacing the 6.5" door speakers and the tweeters with a
5.25" speaker (due to depth concerns), then the
rear 6x9's, and then the
headunit. I also used the Crutchfield harness and adaptors to make things pretty easy. Had to splice in the tweeters, but that was no big deal. Was fun taking off the door panels. Like you, my speaker surrounds were toasted in the doors:
Taking out the headunit, I was very surprised that there were no speaker wires! I had purchased a new
JVC headunit with decent power (RMS), but I guess I will not be using that! I am using the RCA to DIN adaptor to keep the factory amp in service.
I used 2 way speakers in the doors, and 3-way speakers in the rear, and I kinda regret that, too much high freq sound, it's just overly bright, no matter how much I pull it down with the built in EQ in the headunit. iPhone connectivity is great though!
Now that I can fiddle with the system, I discovered that the front dash speakers were buzzing (blown?) and it annoyed me. Turns out, those are hard to replace! There is a metal shield protecting a harness on the drivers side (alarm harness?) right behind the speaker magnet that limits depth to 1.65" Most decent 4" speakers are 1.95" deep. Also, most 4" speakers are 2-way, with tweeters that sit proud of the speaker surround. Crutchfield recommend a
particular 3.5" speaker that should fit, but I found a local stereo shop that had a pair of 4" speakers that were 1.62" deep, with fairly flush tweeters. With these 4" installed, I noticed a significant difference in the audio quality. It really sounds more full and vibrant. Possibly it was the higher quality of these 4" speakers. At $180, they were more than the doors and tweeters combined.
I'm still not content though. So I bought a
powered sub that will connect to the headunit using a dedicated preout. It should fit under the passenger seat. This install will be a bit more involved (more wiring), and hasn't happened yet.