Hi Matt,
yes mines a 9n3, but i'm sure the same. In regards to your questions, i've answered them as best as I can below:
1. What did you choose to do with regard to wiring for rear speakers (my main concern)- did you run the rear right across under the rear seats and then down the left hand side under the plastic fitments to the front? (Along with the left rear speakers' wiring). I'm wondering what the best way to do this is/ what you found worked well.
This was initially my biggest concern too, but it turned out to be much easier than I thought. We first fitted the speakers, there was just some sponge covering the holes and these also had places for the screws. Once the speaker was fitted, I traced the new wire through the doors rubber wire gasket (sorry I don't know the proper name for this, its the rubber thing that all the wiring to the door goes through). This was the hardest part as there wasn't much room for a new wire and took a bit of fiddling before I managed to get it all the way through. Then the wire went underneath the front door sill and into the front dashboard, I then traced this up behind the dashboard and into the back of the stereo. The speakers I got from Ebay also had connectors, which I soldered to the wire so I got a good fit onto the speaker connections.
2. How did you wire the new rear speakers to the head unit- I'm really hoping the main wiring loom does have unconnected wiring which would normally be used for models which include rear speakers. Otherwise this could be trickier.
Exactly as you said. The wiring loom I got to connect the stereo to the car already had the wires needed for rear speakers, the colours were violet and violet and black and green and green and black. The wiring diagram on top of the stereo helped too. I simply cut these and joined them to the speaker wire.
3. Did you find that all four speakers are indeed 17cm/ 6.5''? I understand this is the case.
Yes all speakers were 6.5", and the Alpine ones had many cut outs where they fitted perfectly with the screws in the speaker mounts. One thing to be aware of is that you do need to get speaker mounts for the new speakers and if possible new speaker wiring connectors. These all came with the speaker I got. The old speakers were held on place with rivets, so you have to drill these out. Once done the new speaker screws fitted in the holes perfectly.
Also take a look at this thread -
viewtopic.php?f=43&t=55879 This helped me a lot when I was planning the fitment, I got the wiring loom (PC2-75-4) they mentioned and didn't have to worry about cutting any wires for the stereo to fit (apart from the new speakers)
Good luck!