How do I smooth out violins?

I see the weak points in your system as the Marantz CD player and the NAD preamp/tuner. As a Spendor SP1/2E user, let me attest to their ability to render classical music very well indeed. By the way, I became even happier with the Spendors after adding a good subwoofer to supplement the low end. Classical music is much enhanced with Spendors combined with a sub (same with other music). Bottom line: No free lunch. Your loudspeakers deserve much better electronics.

You know, distortion affects all signals passing through your system.
The nasties you describe are always present, even on the solo violin you think sounds good.
On some of the signals it is more obvious, that's all.
I read a post where someone suggested that the more diverse your system sounds with different source material the more likely that it is neutral.
I think that he is on to something.
All of the distortions in a given system color the sound. Many together make mush.
I have found that the closer I get toward neutrality (non-distorted sound), the larger difference small changes make.
It is like peeling an onion. I keep chipping away and all of a sudden things really start to come into focus. At first it's a leap of faith and then the closer I get the clearer it becomes.
An analogy is color mixing. Too many and you get muddy brown. Narrow the blend and it becomes clearer and brighter. Distortions are like those colors. The more of them you have the muddier the situation becomes. Peel them away one at a time and only after most are tamed does the picture become clear.
-Mike

I notice that in this and related violin forums, nobody mentions the complexities of the human ear. An early very sophisticated attempt to explain vagaries of massed-violins tone is by Mark Dolson in the early 1980s. This paper is not directly useful to improving the sound of your hifi set, but gives you some ideas.  eg, I have many CD on which massed violins sound fine; but I have bought 5 CD of Rachmaninoff's Piano Concerto #2, and the violins are bad on all.  Does Rachy score the 1st and 2nd violins in some peculiar way that creates "Dolson Effects"? I can hear massed-violin problems even at high-quality live concerts, the Vienna Philharmonic, eg. Wall & ceiling reflections can damage massed-violins tone—also, like Dolson, published in acoustics journals.  I suggest that female-chorale distortions arise similarly.  Of course, it is highly likely that the situation gets worse via the processing and playback chain.     

I used to have a McIntosh C50 solid state preamp and swapped it out for a C2500 tube preamp, and that change not only smoothed out violins, acoustic sounds (voices, pianos, guitars, etc.) also seemed to sound more "natural" to me.  Then I swapped out the stock tubes for Gold Lions and that further improved the sound.

Get a better source and add ac filter chokes to your preamp and amp!