Hoping to add some helpful info (and I know a lot of you probably aren't familiar with me since I don't post that often, but I've been a member for a long while)... Referencing the book from TDahl's earlier post ("The Enterprise NCC 1701 and the Model Maker" by N. Datin McDonald and Richard C. Datin Jr. - just so no one has to go back and look it up), there is a mention in the book regarding the hull markings. The markings (at least from what I can remember without having to re-read that part of the book) were painted on for the two pilot episodes. Once the series got the green light and the 11-footer was modified (bridge structure dome lowered, lighting added to the nacelle fronts, etc.), after repainting the model to give it a more weathered look (and add those pencil-thin primary hull lines Gene Roddenberry insisted on, even though Matt Jeffries tried to explain that on a ship as large as the Enterprise you'd never seen those lines unless you were literally on top of it - but as Jeffries added - not a direct quote, but pretty close - 'Roddenberry was the boss so the boss got what he wanted', and Jeffries added the grid lines to the hull using a finely-sharpened pencil); but after the repaint and weathering, they did indeed use waterslide decals (the audio in the above YouTube vid isn't the best, at least not to my aging ears, so they might have mentioned that). They did discover the markings were decals during one of the restorations when they initially thought the letters/numbers were outlined in a "goldish" color; that goldish color, as we are probably all familiar with, comes from waterslide decals' edging as the decals age, and that's exactly what happened to the 11-footer's decals.
And I don't intend to contradict division 6 (never contradict anyone with a name like that unless you want to end up in a nameless dimension and never be seen again), but it also mentions in that book the reversed markings used on the sides of the warp nacelles, so they could "reverse the footage" and make it look like they were filming the left side of the 11-footer - which by now had been torn up for the wires for the lighting and nacelles' fan blade motors - were applied over the existing markings using plain printer paper, as in those days with the camera and TV resolutions they were working with, you would never see the lines on the small TV screen - like we never saw the hull grid lines on the small screen. So division 6 was actually on the right track, the production people just never removed the existing markings from the model; they filmed it with the mirrored markings "carefully slapped on" over the existing markings, and then the footage was reversed in post-production to make the numbers look correct, and make the Enterprise look like she was moving across our TVs right to left instead of the usual left to right.
One final thing I remember being mentioned in the book regarding the nacelles' front domes (what they now refer to as "Bussard Collectors")... When they moved from the solid wooden domes with the spikes on them (and these domes didn't have those three screws/bolts holding them in place, those were added with the new domes so techs could get at the lighting and motors), according to one of the Datins, the new domes were vacu-formed from clear plexi, then taken to have the inside and outside sandblasted to give them an even frosted look. The domes were then sprayed with a transparent matte orange inside and out: the frosting and matte paint being used to stop the studio lights from flaring off of a smooth plexi or gloss paint finish - something Mr. J.J. Abrams should have taken a note from in his overly "lens flared" films.
The name of the color painted on the new domes was not specifically mentioned in the book, other than "orange". So the dark orange paint Mr. E Man found looks like a good match to the orange we saw on TV in the odd times when the nacelle domes were seen unlit (and I can't remember which episode - or episodes - that appeared in, but it was not often). It's difficult to reference those images now unless you've got a DVD set of the original 'Trek' from years back, as the sets you can only seem to find now are the re-mastered ones where the "Big E" is all CGI. But since the book says both the inside and outside of the domes were painted, I would suggest getting the orange that Mr. Man suggested, as well as your standard, plain transparent matte orange, and test both on some scrap plexi (or whatever you plan to use for your domes) and see which looks better to your eye - or what matches the color on the original non-re-mastered unlit domes - to see which works best for you. (I'm not all that familiar with 3D printing "clear" things. My son is the 3D expert, and he says that "clear filament" looks clear, but when you print with it the item you print will have a frosted look to it. The item can be made to look as clear as possible by carefully using acetone - nail polish remover, or so he says - on both sides to make the printed object as clear as you can get it, considering the inner thickness of the object's walls can't be gotten at.) But again referencing the aforementioned book, since both inside and outside of the domes were sandblasted to make them frosted, you probably don't need to bother trying to make them look "clear" only to make them frosted again. (But sanding a scrap piece of plexi on both sides and trying the paint on that should save you some filament.)
Anyway, I hope my blithering has been of some help.
Dino.