Glenn,
So you are going to buy a NAS have it controlled by the DSM-540 and the both will interface with twonkyvision.
Have you used the DSM-540 yet? When I used the unit it would not play the albums in numerical order it played albums in alphabetical order. You can use the MX3000 remote as you will have to learn the IR codes from the DSM-540 and watch what you are doing on your TV Screen. If you take a look at the Nevo remote thru the Wi-Fi it will also control the DSM-540 and will even show the photos and album art (the Cover of the CD) on the screen. I am not sure about it displaying the movies.
http://www.mynevo.com/ Zach