Ok.. here's the poop..
The original D2A was upgraded to Mk2 status to take advantage of an enhanced low jitter input circuit (which at the time was quite unique).
I suspect what you are hearing is the added jitter from your NAK transport. If you can try a different transport.
Sean has a valid point, try some different cables. The best one I found with my D2Amk2 has been the MIT Digital Reference (with the nodule on it).
IF your original D2A has the small power supply (not the triangular IPS) I would suggest that you source one FAST !
It will make an enormous difference.
I think that Aragon may still offer an upgrade for the original D2A that you have. Check on the Mondial website, although since they've been taken over by Klipsch you may have to wait a bit for service.
The later/current D2A2 was a compromise to bring out an HDCD ready DAC to the market, anyone will tell you that the earlier DAC was far superior in handling standard CD audio.
As a matter of fact, I have compared this DAC to even the Levinson 360 and it can still hold it's own. However, the 360 becomes a different animal when run balanced (which it should be.. you don't know what you're missing !) at which point it eats the older D2Amk2.
Hope this helps.