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So as you guys may or may not know, I'm working on a Militarum Tempestus army meant to emulate an old themed army I found called "Imperial Navy Drop Troopers."
Now I'll be posting pictures of the units I paint, of course, but I'm running into a problem with figuring out the colors to use as in the post on it I'm left with only three colors and want the army to both fit the wide arrange of . Shadow Grey as a main color, Chaos Black for stuff like the boots or belts, and Boltgun Metal for, well.. anything shiny. As I'm sure you know, the Militarum Tempestus Scions have these gold parts on their armor, and have a sort of off-greenish color on their guns, and then there's the fatigues. I don't want to make the guns and fatigues match the armor but the standard colors used stick out too much, and in the case of the gold parts I don't want to use Boltgun Metal but I'm not so sure about keeping in gold(this is the Imperial Navy after all). Sooo... what colors should I get for those parts instead of the standard colors for Scions? (apologies if this makes no sense)

Perhaps a blue-grey or something based off Kantor Blue? For the gold you can perhaps use a darker bronze or a bright silver (brighter than boltgun metal to make it stand out).

Take a look in the Codex and see if any of the colour schemes in there inspire you.

I would go with a navy blue for the uniforms. It is fitting and it would contrast well with grey.

I would use copper for the 'gold' bits personally.

I'm voting with these guys above. I like a navy blue. A lot of militaries in the past went with bronze, brass, or copper buttons so I think any of those for the highlight pieces would work fine.
Just for reference, I have an army using Mordian and bronze together. One unit has mostly black as a base as well. Here is a link to the gallery so you can decide. Page 1 has the Rough riders with blue and black. Page 2 has my officer of the fleet and my take.

http://www.dakkadakka.com/gallery/images-102599-50896_Sisters%20Of%20Steel.html