I completed the stereo upgrade but did not take pics for a write up given that the links posted here by others do a very nice job of it.
I ended up putting Kicker 6.5 components in the front, with the mids in the doors and the tweeters in the dash location. The crossovers are hidden behind the kick plates on each side. I also bought another set of the Pioneer speakers I had put in the rear door and installed them in the rear lift gate.
I put a 4 channel amp under the driver seat to power front and rear speakers, and put a 2 channel amp under passenger seat to power sub in the trunk. To get the input into the driver seat amp, I initially used a set of Rockford Fosgate high-level to RCA connectors. But I was not getting any sound in the front and intermittent sound in the back. After much research, I ended up taking those out and using instead Scosche LOCs (line output converters) and that did the trick. To feed the 2nd amp, I used the pass-thru RCA jacks in the driver seat amp. I connected those to the front and rear speaker wires, ran RCA cables from there to the amp under the driver seat. From there, I ran speaker wires back up behind the head unit for the rear speakers, and ran new wires up the door sills towards the crossovers for the front ones.
I kept the Entune head unit for now. I could not find a wire for the blue amp remote turn on, so I connected the amp remote turn on wire to the cigarette lighter that's underneath the center console.
The sound quality now is so much better than with the paper speakers. And the best part is that there it has a complete stock look.