Kamyio, are you aware of the Pulfrich effect? What you're doing with the red/cyan overlays can be simulated psychovisually by wearing a pair of "half-shades" - putting a dark filter over one eye (you can even experience the effect simply by squinting one eye) and watching any normal movie.
The brain processes the dark image more slowly, so your brain ends up combining, say, frame 1000 from the left eye against frame 1001 from the right eye. The beauty of this system is that you don't have to worry about colour filters or compression artefacts - in fact, you needn't do anything to the movie at all.
I don't think anyone's expecting you to turn Star Wars into an Avatar-like 3D experience, and I salute your enthusiasm for trying something different, but I just really don't see how it could work. For every shot where a lightsabre swings out of the screen towards you, there'll be another where it cuts back into the background, ruining the 3D effect.
but I am researching to find the answers on what older 3D movie production companies did.
If you're referring to previous waves of 3D-mania (in the 50s and 80s), they shot them stereoscopically, just like a modern 3D movie, but with more giant ants and less smurfs.
PS I think the red problem with the uploaded video is probably down to compression - red is easy to sacrifice because it's normally not so important to vision. Green, on the other hand, is the most significant colour, so it will be preserved more accurately. A side-by-side YouTube video with the 3D flag would solve that.
DE