I dont see any difference between the 999 and the 1000 either now that you mention it. Same components for each are listed on the website.
As far as the M5's, they are decent stuff for the money which is what Mark typically aims for, they are of course no longer made and have been replaced by the M6 series. For a few extra bucks you can move up to the Diamond Hex series. Or you could completely dismiss Diamond and go with many other products, but no doubt Diamond makes decent gear for the $$$.
As far as head unit sound quality, with a decent head unit (which the NSX has), the key elements to good sound are the speakers and quality amplification (neither of which the NSX has) as well as installation. Once those pieces are upgraded, honestly I doubt you will notice much different swapping out the stock head unit for something else. The main reason I'm interested in swapping is simply features. I want a head unit that displays MP3 titles and such. I suppose I could always keep the stock head unit and instead install something like the Alpine AiNet changer control that offers that feature. Haven't dismissed that possibility yet either but I hate the idea of having to interface it via FM on the stock head unit. Then again we're talking MP3's and not Telarc CD's so it's probably not that much of a big deal.