1. Since you mentioned alignment, there are processors out there that you can plug an
ipod directly into. Just make your playlists ahead of time so you don't kill yourself searching for songs. Or you can get Alpine's iPod Head unit controller that has the BurrBrown convertors. I've heard .wav files that I'd be hard pressed to differentiate against the OG source.
2. I've heard systems with stock locations that sound fine. Mind you, not world class mind blowing great but really good sound/staging. The funny thing is that they were all Honda's. There might be something to their doors and deep dashes.
3. Corner mounted Sub?
4. 5/6 channel amp? There's lot's of them available.