I actually figured a way around the color issue - if I use the RGB sliders instead of CMYK they show up correctly and stay that way.

However I am still trying to figure out how to save my custom colors and fonts - is there a way to just create a custom theme and format all the styles in one window, or a way to save styles you've already used in the document (also to label font styles as a "Heading", "Body Text", etc)?

I don't know if it helps but I've attached a rough draft of the document just in case.