I don't get any noise problems wiring the iPod through aux input. I can't really tell the difference from the iPod and a CD burned from the same MP3s on my Nak.
Mine is in 2.0 ft^3 tuned @ 33hz, and it gets pretty loud and sounds good. I may tune a little lower eventually though. In a sealed box it just didn't extend into the low frequencies as I wanted, they really shine in a ported box.
The CD-700 is awesome but very expensive... if you don't mind buying on eBay you can get a CD-400, which replaced the CD-45z which I have, for ~$280 shipped. I'm sure they have a Nak dealer somewhere in America that sells their car audio... I'd email them...
Tang Band makes a 6x9 midbass / sub, never tried them tho, but have heard good things. Or you might be able to put a 6.5" round mid in.
http://www.tb-speaker.com/detail/1208_03/w69-1213S.as
http://www.creativesound.ca/details.php?model=W691042
I have a blown one, I took the allens off too remove the cover and I still couldn't pull it off, it's glued on as well, and it seems like it's screwed right into the bottom of the magnet, so removing the cover wouldn't really make it any less deep.
A few really high end head units have digital fiber optic output to an exteral d/a converter, for reduced noise. Like Scarenius said it still has to send an analog signal to the speaker, which should be able to be used with high level inputs.
I know of the JL6W0, and Tang Band makes a 6.5" sub that's supposedly pretty nice for the $36, although I've never used them...
http://www.partsexpress.com/pe/showdetl.cfm?&DID=7&Partnumber=264-832