Crutchfield,
sonic electronix, and
online car stereo are going to be your best bets besides your local trusted audio installer as a source of components.
Sonic Electronics and Online Car Stereo are going to have the best prices, while Crutchfield has some good resources and research, though they don't mark down their prices much. For example, Cruchfield was selling JBL MS-62C 6.5" component speakers (good pair of components, btw) for $300/pair, same price as the comparable Alpine Type R components. Sonic Electronix sells the same pair of speakers for $179 with free shipping, and Online Car Stero sells them for $189.
Also, for what you want, you probably want touch screen, good pre-outs and a decent amplifier, speakers, and sub.
Question is do you just want a modest sound improvement or do you want a reasonably priced SQ build?
For a good, modest, budget-conscious audio improvement, I'd go with OEM Audio+ and get a compatible Pioneer AVH/AVIC headunit (ask OEM Audio Plus about which ones), as Pioneer has very good iPod/iPhone interfacing (not so much good Android interfacing until this year's NEX units, and this year's single DIN HU's which are MTP protocol compatible) and excellent sound processing.
This would probably be an excellent HU for you, based on your so-far specified criteria, and would work with an OEM Audio Plus system OR a custom system:
http://www.sonicelectronix.com/item_...-X5600BHS.html
Sonic Electronix has some of the best balance between pricing and availability, I'm finding. Though I'm looking to add another amp to my system and upgrade my rear speakers to 6.5" coaxials. For that, I've found the stuff I want at online car stereo for less than $300 total.