Crutchfield has always been helpful for me, along with the car audio forums. Here's the car audio stuff I went with. I'm no guru, and there's probably better stuff out there, but I'm very happy with how my system sounds.
I don't want to give too much away too early, but here's what I ended up going with for the stereo.
Head unit: Alpine CDE-HD148BT - I wanted something with 3 sets of RCAs, 4v pre outs, excellent sound, bluetooth, and excellent control to tweak crossovers, sub levels, time delays, etc.). This ticks all those boxes. There are way cheaper head units out there, but I'm very happy with this one. I'm more interested in how it sounds and how I can tweak the sound than the color it displays, or how it looks. I like being able to control pandora on my phone through the head unit. I can thumbs stuff up and down, skip, switch to another channel, etc. I also wanted one with HD radio, since we'll be traveling a lot and I like to listen to different radio stations across the country. I researched hundreds of head units before coming up with this one.
http://amzn.to/1FPVg88
Speakers: JBL GTO 8628 - My 4runner had a factory JBL system in it, and it sounded incredible. So I took a leap and went for JBL again on my speakers. For the price, I'm very happy with these. I wish I had purchased something with a little more power rating though, since the little Clarion amp can overpower them (since the Clarion has 75RMS @ 2 ohm). But I don't turn it up that loud anyway, so maybe it won't be an issue. They haven't broken in yet, but I'm pretty happy with them. The price is definitely right. Without a sub I'd be disappointed since they don't have a ton of bass, even with an amp. With a flat EQ I don't love them, but when I EQ them right and blend them with the sub, they sound fantastic.
http://amzn.to/1OQLUMi
Speaker Connectors/Adapters: Metra for Ford. Very convenient.
http://amzn.to/1FPWnov
4 channel speaker amp: Clarion XC1410 - I'm VERY happy with this. If fit behind my dash. It doesn't have many controls though, which is why I wanted a head unit that could handle all the crossovers and levels out.
http://amzn.to/1OQLKoc
Sub: Alpine S10 - (I like punchy bass more than boomy bass). Paired with the m-500 amp, this thing is amazing. I'm still fine tuning the EQ, but I'm very happy with it. Insane power handling.
http://amzn.to/1hj92EG
Sub Box: Scosche Se10 - Pretty well made. I wish it were one inch shorter so it would fit under my middle bench seat, but I haven't found any 10" sub boxes small enough to fit underneath the seats anyway. I'll end up building a spot for this in my interior eventually
http://amzn.to/1FPVCeZ
Sub Amp: Alpine M-500 - I think it's better to have too much power than not enough. This thing is nice and small. With some trimming of the interior panels, I was able to get it to fit behind the side trim panel on the driver's side, halfway back. This thing really is a small amp for 500 watts. I'm super happy I went with this amp.
http://amzn.to/1KZrQl0