So, there are only 3 photos of the main shooting model that I could find that pedate it being loaned to Magicam whatever they did to it.
Held by Matt Jefferies himself.
In this photo you can see the multi tone finish. The markings make it clear this is the first model (The 2nd model has an extra character). The main body is darker, but the top of the head is not (unusual). You cannot directly see the lower color vs. the neck/head color, but both are lighter than the upper body.
This photo from the AMT box art.
You can see from the side of the engines that this is the main model. It has the two bars on each side of the engine and has the right markings. Here you can clearly see the color of the markings. The white and yellow are distinct colors, though the two lower arms of the logo (or left arms since this was before it got rotated) are dark and hard to distinguish. You can also see some of the color differences. The pylon is darker than the engine. The lighting is extreme and obscures some details, but this is a color photo of the model.
This photo is from after the series while it was at the Smithsonian. I think there is another one in color form the front. If anyone has that from a pre 1978 source, please share. But again you can see that this is the main model due to the markings and the engines. The engines are lighter than the upper body. You can see in this photo that the grille on the pylons is not silver but the upper hull color. The head is lighter than the engines, but whether this is from it being a different color or the lighting who can say. The colors on the Klingon emblem make it clear that the long point is red and nearer small point is green, but otherwise all you can see from this is overall tone differences.
This screen capture from the original TOS also shows lighter engines, head and neck, darker upper body with painted grilles. It has been processed enough that you cannot make out the individual colors.
This screen cap doesn't really reveal anything except the marking on the bottom, but it is a cool shot. Not sure if everything in this shot is the same color or if the color difference is just obscured.
We can verify the time period in a number of ways. This is 1701 before her 91 refit. That of course is a young Gary Kerr holding the D-7 (note the scale matches the photo of Jefferies holding it). But we can see colors now. But we are also post Magicam. We can compare the colors of the model to skin tones and the 1701. This is the photo I think best shows the colors of the model before Ed Miarecki repainted it. He repainted it based on a color photo of how it was sent over from AMT. In this photo it is clearly 3 colors with the neck being gray, the under body and engines being green and the top with a hint of purple. You can also just make out the color of the markings and see that the characters are lighter than the circle.
And in case you are wondering what the issue is with Magicam, this is how the returned it. It was sent to them intact. Lots of question surround what they did to it and what they returned. You can also clearly see the different colors, though I think they appear too dark here. Again, the circle is darker than the characters. The one arm you still can't tell if it is black or blue, but it is definitely very dark.
And this is why Magicam took it apart, to make these pyro models for the Phase II pilot that became TMP. The explosion was still in the early scripts before they changed it to the Klingon ships getting scanned. A few of these pyro models were exploded, but one was around for an important step later.
So, this is the main model after Ed Miarecki repainted it next to the Phase II/TMP model. You can see how faithfully they copied it before they started updating it. But it is a general light gray with silver grilles and details.
And here is where that inact pyro model made by Magicam comes in. This is a copy of it. This is the D-7 Gr'oth from Trials and Tribbleations. Note the completely different Klingon script. All the formerly silver grilles and details are a goldish copper. The marking is very yellow, green, blue, and red. The hull is azteced like the Phase II model and it has some additional markings (a yellow line and some red pinstriping - literally red tape). A modeler could achieve this look by painting the model gray and then penciling on the lines and highlighting them with some gray pastels. But you can see how good this copy of a copy is. One worry is that all or part of what was returned to the Smithsonian is not original. Both the models should have been built the same by the AMT builders, but no opportunity to compare them has come up. But what Magicam did raises a lot of questions about the model that the Smithsonian has had since that preclude any certainty as to how accurate it is.
The second model appears to be original. The markings look how I would expect them to after being on display so much over the past 50 years. The yellow of the circle has faded and the white of the Klingon characters has yellowed. For someone who has been modeling for 40 years and has some models that old, such yellowing and fading is not to be unexpected. And we don't have any good color reference photos for it. All the photos I have been able to find show evidence of heavy color distortion from the lighting conditions. That photo of it being held by Gary Kerr, provided those are the true original colors, is the best available source. Mainly due to the Enterprise in the background which we can easily compare the color of to other photos. And these colors match in tone to the photos of the second model, but on that model, under the poor lighting conditions, you can't tell if it is in 2 or 3 colors. My best guess for the colors, based on all these photos, is that the current gray is the correct color for the neck and head, the bottom of the main hull, aft end of the neck, and the engines should be a gray/turquoise color that is a hint darker, and the top of the head and the main body, including all of the outside of the pylon, should be a slightly darker gray with a hint of purple to it. Highlighted by a dull silver for most of the grilles. If you go by the 2nd model, there would also be some chrome (the center upper grille and two grilled areas on either side of the base of the neck).