When you were testing your Ipod, did you have it hooked up to a charger?
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It shouldn't make a difference, since you the Ipod is getting ~5v rather than directly powered from the vehicle power supply.
Various models of Ipods and other media players can have wildly different frequency responses, even though it sounds 'ok' through headphones.
http://blog.faberacoustical.com/2010/ios/iphone/ipod-touch-3g-headset-io-frequency-response/
Edit: above link is showing the mic input frequency response, but I will keep looking for the data on the output voltage and frequency response.
I've had it both on and off the charger. I wasn't keeping track though, so I couldn't really give you more detail than that. I didn't have it on the charger at any point today though. It may just be the power of suggestion, but now that I think back it does sound better (cleaner but not any louder) without the charger. It also sounds better with the engine off and just sitting in the driveway than out on the road, but that's probably due to the lack competing road noise more than anything else.
Just earlier today I was sitting in my truck in a parking lot waiting to meet someone. I was listening to the ipod with the engine off and the key turned back in the "acc" position and it sounded fine. I was listening to Everlast and it was playing the full range without much noticeable distortion. It's rap music but it's bluesy with a lot of acoustic guitar, the guy's got a gravely voice.
Here's a few songs of his, for reference:
https://www.youtube.com/watch?v=x8YV18njbSg
https://www.youtube.com/watch?v=DSRHi79XdsM
https://www.youtube.com/watch?v=vPoEA43cqKc
That article on Ipod frequency response is really something too. I've got an Ipod Classic, circa 2007 or so. I wonder what the output looks like.
When I get the chance I'll pull the radio and re-check all the plugs and make sure everything's clean. Also, while I have your ear, what do you think about speaker cups/baffles? I think it would distort it since that's not how the speaker was designed to run but I'm looking for something to protect it from any water that gets in the door. I live on the coast and it's always wet here.
People claim lots of things about how it effects the sound, but I would image that I could cut the bottom 1/4 out of it and that would allow it to operate in free air as designed, but still provide decent protection.