I haven't done anything drastic to my minis, and likely won't - I want to keep the "look-n-feel" close to the film canon.
That said, I've started adding triangles of Citadel Blood Red to my TIE fighters, and will find a way to add unit markings to each model so they are all individuals. The red isn't working very well against the black of the TIE's solar panels though, so it'll need at least another coat and probably more :/
Also I've used Citadel Foundation Blue (Mordian Blue?) to replace the red on one of my X-Wings - and made it "Blue 5". Sadly, this particular shade of blue lacks "pop" on the table, so I'm probably going to clean it off and try Citadel Snot Green instead. Oh, and I've used Citadel Iyanden Yellow on several panels of Blue 5 which adds flavour.
I'm considering a complete repaint of an X-Wing fighter as well, just for the fun of it. If I do so, I'll start with a white undercoat and work up from there.
Painting a bright color over black is tough. Here's a couple of techniques I've used in the past to varying degrees of success-
Probably the easiest of the suggestions I'm going to make is this- paint a layer or two of silver metallic (probably the lightest silver you can get your hands on) on top of the black you eventually want to turn out red. After that dries, wash it with an ink or wash in the color you want. If that's still not quite there, try layering on a third coat of a regular paint color. A light grey can work in this application as well. I painted up some Terminators a couple of years ago that I wanted to have a quartered black and white armor pattern. I decided to prime them grey rather than black or white. Worked famously and I found I had to do several fewer layers of bright accent colors for pad trim, jewels, lights, and those other doo dads that are usually bright points of color because I was only working up from grey.
Secondly, you mention Foundation paints- try a base layer of whatever they're calling Merchite Red these days, then layer on a brighter (i.e. your Blood Red) over the foundation layer. I don't know the paint color names since they switched them this last go around, but whatever the red foundation is. If the idea of doing two coats on such a small surface is daunting, mix in a little bright red with the Foundation.
Third, and this is what I do on my red accented Necrons, so it may not exactly be the look you're going for- do the silver coat as above, but instead of hitting it with a red wash, try a coat of Tamiya translucent red over it. On my Necrons, it yields a different sort of look than paints, inks, or washes. long story short, it almost kind of looks anodized.
Anyway- just some food for thought. Good luck!