My wife has an 06 convertible. I hated the Shaker 500 so much that I wound up replacing every component in the car.
1. Dynamat the entire interior space.
All sides of the truck space including the lid.
Removed the carpeting and replaced with better quality and went with Black vs. Lt Grey.
Dynamat is also on the floor pan to kill road noise.
2. Took out the rear seats [useless in the Mustang to begin with] and built a rear seat delete. The bottom shelf area has boxes for 2 x 10" JL Audio W3V3-4s. These are sealed not ported and face upward not toward the driver.
3. The Mach 1 and rear area 5x7 are all gone. Replaced with JL Audio C3-525 component speakers and external cross-overs.
4. The 1" directional tweeters are placed in the top of the door panels by the mirrors in front and at the top of the lower interior trim panels in the rear. This is right under where the seat belt retractors are. Basically, they are about a foot from your head so you can hear them very clearly.
5. The backboard of the rear seat delete holds a 4 farad capacitor with digital voltage meter and also the power and ground distribution blocks.
6. The back also holds both amplifiers. I used a JL Audio XD400/4 for the 5.25s and a XD600/1 for the subs.
7. The head unit was replaced with a Kenwood DNX9990HD. This unit has everything including 2 USB ports mounted in the center console and a SD slot for updating the NAV maps. It has live traffic and your choice of sat radio. Front and Rear 13 band EQ and is in dolby 7.1 surround. It has 3 AV feeds and outputs so the last item will be placing a 27" LCD on the inward face of the rear seat delete boards.
8. Add the wiring harness, mount kits, nicer face plate, antenna amplifier and another antenna for GPS.
My latest additions:
9. The 8" stock door subs are being replaced with 8" JL Audio W3V3-4s so everything matches. I'm also planning on line feeding another XD200/2 to power these.
My wife thinks the whole thing rocks but my tuned ear says we need just a little more bass at the higher end up front. The 8s will do just fine.
If you pair it all together and know what will sound good, it becomes all about mounting location. Our outfit rocks seriously hard and clear. I barely use the dual 13bands. We basically run it flat since the LPF and HPF send signal to the cross-overs. It's already tuned and doesn't need additional tweaking.
I posted pictures on photo bucket but haven't taken one with the Kenwood installed yet. I also need to add a few showing how the rear boards have the amplifiers mounted.