06 gt entire system help

My mustang came with a Shaker 500 but I don't really like the sound...I think I want to completely switch it out to a better system. Is it possible to get a really nice system (with more bass than the factory, and louder sound too) for a few grand? That's about my budget but if it takes more I can save for a while, I want to do it right. If you have any recommendations, I'm looking through all the "Higher End Brands" in the FAQ section. Is it better to get all the parts through one company or is mixing and matching no problem?

Also, I'm not sure about the headunit--is it possible to get something that plays MP3's without having to put a cd in (like an in-dash ipod, obviously looking nice like a normal stereo though).

Thanks in advance for any help you give me

Here's what I had in mind, tell me if you recommend changing any of this etc.:

Amplifiers
JL Audio 300/4 amp for speakers
JL Audio 500/1 amp - 4 ohm - for subs

Subs
2x JL Audio 12W3V2-D2 - 2 ohm each 4 total

Speakers
Focal 570CV1 5x7 for the back
Focal 130V1 5 1/4" w/tweeter + mounting plate for front

Headunit
Alpine CDA 9856 headunit

I still don't know what to do about boxes and getting a mounting plate, but that's where I'm at now. Suggestions?