First, give it a break and enjoy running some routes or something not paint-related for a while. Then come back to your project and create some additional layers in your template so you can assign different colors or combinations of colors to each of those little parts that are driving you nuts (hinge plates, nuts, bolts, etc). When you run out of colors, you can also incorporate geometric shapes to extend the pallete. I typically use stripes, polka dots, and squares of a variety of colors to further extend the available combinations. I usually assign geometric shapes to the larger parts, and stripes to the smaller parts like nuts and bolts, since the geometric shapes are too big to fit into the smaller items.
Even with this technique, you may run out of color combinations soon, so just do a section at a time and run it in the sim to identify where each little part belongs and take notes along the way. You can annotate the locations in your template, but with as many parts scattered about on this particular model, it might be best to make a diagram on paper and label the locations. As I recall, there are several texture files containing these intricate details, so again; pace yourself and work sections at a time until each of their contents are identified.
I recall when working on the VRC u-boat models (also with numerous details) I must have taken what seemed like over a thousand screenshots before I had everything identified. The only problem I ran into was a single hinge plate that was shared between two different areas with different colors, so I had to choose the color least likely to be noticeable to the rivet counters. So don't be surprised if this happens; sometimes parts are shared and there's nothing you can do but select the lesser of two evils.
Lastly, if this all works out; make a key-chart for the rest of us painters who currently don't have the time nor the patience to partake in this madness
Of course, there's always the option of contacting the developer, who may already have a chart available; but that would take all the fun out of it, right?
Enjoy your project, try to stay sane, and good luck!

(Btw, for those reading who are not familiar with this model; I'm not knocking it when I say "parts scattered about", because this really is a highly detailed model and it's obvious the developer put a lot of work into it. It's just that for painters, all this detail can sometimes be a nightmare when producing multi-colored re-paints. Monotone jobs don't require all this work, since all the little detail parts can be the same color, no matter where they reside; the only factor for consideration being the intensity of the weathering, if any, in certain areas. I suppose it's akin to comparing construction of a 300 piece jigsaw puzzle versus a 5,000 piece puzzle; but in the end, it's well worth the price of admission to see the final product running in the sim.)
As an after-thought, here are a couple of WIP shots to illustrate the parts identification process:
SD45_PanelFinder_01.jpg
VRC_Uboat_nuts_bolts_01.jpg
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