1) It comes with 8 speakers, 2 in each of the front doors (one tweeter and one speaker), one in each of the rear doors, a center channel speaker on top of the dash board just above the headunit and a subwoofer in the rear cargo area on the passenger's side.
2) No, the NAV system is only available with the 8 speaker system.
3) Yes it comes with a subwoofer.
4) I haven't listened to one yet, so I can't help you there. I do have an E7007 sitting it a box that I haven't installed yet (same unit as the E7008, but used in the Sienna). What attracted me to it was the 4-disc built-in changer with MP3/WMA playback as well as the lane guidance (it tells you which lane to use), voice commands and bluetooth. Also, I like the stock look of it.
5) Not too familiar with aftermarket NAV's, but you could go with the Solara NAV off
www.oemvalue.com. To do this, it would be best to get the 6-disc JBL Synthesis unit with your 4Runner since the wiring will be in place and you will already have a digital amp. Of course you will need to get a different trim piece for the radio if you do this. I've also heard good things about Eclipse NAV's, which are made by Fujitsu-Ten, the same company that makes the Toyota NAVs. They have pretty similar features. I've also heard good things about Pioneer NAV systems.
I hope this helps you out a little bit.
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2003 4Runner SR5 V6 4x2 - Pacific Blue Metallic/Taupe Leather