Not that your system is exactly crying for an upgrade..but if you insist, I would look at a tubed CD player, like Audio Note or the new Shanling for a better sound from the digital quarter, as it will be hard to improve much on the Genki with another solid state cdp.
Your analog setup also has room for growth. I would probably sell the Project and BluePoint and buy a mint condition Linn LP12 I have available...oops, cheap plug. But seriously, if you listen to records very often, a Kuzma Stabli with a similar step up in cartridge quality would be the way to go. They are quiet and untouchable under $ 2K.
Of course, a good tube preamp and phono stage instead of the NAD would do wonders. You might try this hybrid route while keeping the Krell for its bass control and authority. Also, I did not see a record cleaning machine like a VPI or Nitty Gritty, a must for getting the most out of your vinyl(my next purchase in fact.) Discwasher or even Last do not come close to doing the job.
I love Nakamichi for cassette decks, and I think someone(not me) has the legendary Dragon listed for about $ 850 on the site. If you don't buy it, I might. Nothing else ever came close. At least you have a Nakamichi, just not THE Nakamichi. :-)
All in all, a very well thought out and balanced system,
but if you are still not satisfied(are any of us?) than warming up the sound with a tube pre might be the trick. Not knocking NAD - I own two. But I was blown away recently by an audition of a modest system consisting of the Manley Stingray/ProAc D15's/Audio Note CD3(CD4?)/Nordost Solar Wind at Arizona Tube Audio. And I have almost always owned solid state equipment, thinking tubes were too much hassle and too bass/power-shy. Scary to think they could well be worth it!
That is why a hybrid system may well do the trick. I believe the Velodynes are self powered, so you have some options here, although the Dynaudios probably like a fair amount of power to open up.
I am in a similar quandry, and am looking at tubes as a possible way to make the most difference, short of changing transducers.
Let your fellow Audiogoners know what changes you wind up instituting.