Hello Rickard,
I share your interest in GT's. I have the Trumpeter kit and am about 60% complete with it. Like you I did not want to model chassis 1046, the black restored car owned by George Stauffer which Trumpeter used.
I have collected over time, a fair amount of visual research and learned that 1046 which won LeMans in '66 has some differences with the way it was restored and how Trump modeled it. I am aware there are a few other decal sets available for other cars in '66. But here's the catch-each of these cars were different from the kit version we have. Things like oil coolers, interior arrangements, suspension parts, wiring and fuel pumps are slightly different car to car. If you are not concerned with accuracy, you can build the kit and put different colors and numbers on it.
If you do want an "as-raced" replica I advise you to do extensive searches for the various chassis numbers, collect the photos and be prepared for a lot of scratch building.
As I learned all this I decided that the kit had too many construction compromises in it to be an exact replica of any of them. Trumpeter only "suggests" the look of some parts and omits others they did not wish to engineer-like a distributor and wiring and brake plumbing. Most of the suspension and oil and fuel lines they include suggest the original but are only representations at best. The springs, brakes and suspension arms are terrible with toy like connectors. They include an interior roll bar structure which is how it was restored but it did not race with one at LeMans.
So I decided to go another way-I'm building a car that didn't exist but is in as-raced condition. Sort of like a test or practice car. I selected a silver-blue metallic color (very much like Viking Blue used on Cobra team cars) with no markings. My car will be "weathered" to look like a heavily used track car. I have scratched new suspension arms and some joints where visible and did a lot of interior wiring and piping. I spent an enormous amount of time reworking the tire profiles (which are all wrong as supplied) then painting and lettering them and the wheels. Many parts are not visible when the car is complete, even with the nose and deck removed.
Trumpeter did do an excellent job on the fitment of the parts-except for two important areas: the doors are bulged slightly above the roof at the top and the entire rear deck does not lie flat on the top outer edges. I tried some heating and bending with water to no improvement. I see now why many modelers on other forums complained it was too expensive for what they give you. But I am a lover of GT-40's and this is the first ever 1/12 so I had to get it.
Well I did not answer your question but I would love to hear your thoughts on your project. I have enjoyed the challenge to my skills and matching the details to my research pictures of the various cars.
Cheers,
Merlin