I don't see a problem, as long as your not going to try to eventually sell it as a real SS.
For the '66 SS, there are naturally the exterior emblems and the hood with the scoops. There also is the emblem above the glove box. The rest of the trim inside is the same as the Malibu. Facory guages, tach, bucket seats, etc inside are all the same as what is optionally available on the Malibu. These parts were optional on both SS and Malibu.
Under the hood, the frame-side motor mounts are different, bur small block or solid block-side motor mounts could be used with the Big Block. The passenger side front brake line is also different, crossing over the frame closer to the firewall than a smallblock car. This is for extra clearance from the exhaust manifold.
The SS always had a 12-bolt from the factory, and there are a few extra frame support brackets for the rear suspension pickup points, but these, as well as the brake line are often overlooked.
So really its the hood, emblems, rear end and engine that make the SS. You could have bought an SS with a bench seat, column-shifted powerglide with no gages (although I don't know why someone would.
I have had many '66 Chevelles. I currently have a cloned SS and a real SS. I have more fun in the cloned car, because I am not worried as much about parts breakage or modifications. I am even contemplating selling the real SS to help pay for some more modifications to the clone.
Of course, It all depends on my mood as to whether I'll admit its a clone or not. If I realize its someone who is truly interested in Chevelles, I will usually tell them its a clone, but if they are those "I had one of those when I was younger, what year is it?" kind of people, I tell 'em its real. So have fun with the car... do what makes you happy.