RE: Shaker 1000 Warranty Replacement?
I have the same car, in blue, and the first thing that I did when I bought it, was remove the entire audio set up. With the top down it just did not have the juice to listen to music while driving.
I would suggest replacing the head unit and all the speakers, and getting seperate power amps to push the speakers. Also, MTX and JL Audio (if you want a higher end unit) make form fitting subs that fit in the trunk to replace the Shaker 1000 system. I know it's your money I'm spending (LOL) but it looks like you already have done a lot of great work to the car, and this just adds to it. Also, audio eqiupment can, and should in most cases, be bought used (head units and amps always, sometimes subs and speakers) and then if you decide to sell the car, and you don't think you will get any love for the extra audio gear, put in the factory stuff and sell the gear.
Anyway, the new Ford head units are supposed to improve tremendously over he next couple of years, but I think they will still be a step below the aftermarket.
For head units, I would suggest a used, or new and very discounted Alpine IVA-310. It has a flip-out touch screen, DVD player, direct inputs for an Ipod (controlled through the screen), Sirius, rear camera, and Navigation (either Alpine's own or others), and they have gone way down in price.
I also like the new Alpine digital amps. They have a ton of power, and run very cool, so they don't over heat and shut down if you are on a long trip.
Speakers are a personal choice, and in a drop top, it's not like you are in a dedicated listening room or home theater in your house, so power handling is usually more important than clarity. Alpine, Soundstream (good choice for LOUD), JL Audio, Boston Acoustic....
lots of choices..
PS - they replaced my top on my car as well. Mine had some slight fraying, and they just changed it out. I was very happy about that.
2006 GT Convertible Vista Blue
Whipple HO Supercharger Polished