Well, I guess I'll throw in my $.02 here.
(1) I can't say I'm a big fan of Sony. I just hear way too many failures of their equipment (except for the high-end stuff, which is exceptional). There's so much stuff out there to choose from. My next HU will probably be a Clarion, well built, clean looks, and good performance.
Get some custom components like Aaron suggested. See this
link. They will outperform the Pioneers handily for $58. They will really sing with a moderate amp.
(2) Personally, I'd put it in the trunk. Less chance of theft and less chance of somebody damaging it with an accidental kick. Just make sure you disable the manual trunk release.
(3) Definately get the "generic" dynamat from McMaster Carr. For $100, it'll make your car much quieter and your stereo sound much better. I'd avoid the waterproofing baffles. They'll probably negatively effect the speaker's sound. I can't say I've ever had or heard of anybody with water damage to their door speakers.
(4) Call crutchfield and get their installation kit. It's got everything you'll need along with very detailed instructions. Best $20 you'll spend on your installation.
Good luck!
-C
