What you are doing wrong is I think a misunderstanding of what you expect. A One Shot Colour(OSC) camera captures colour images but you need to debayer to get the colour. What you are doing is capturing greyscale (or black and white if you prefer) through colour filters. All correct so far. Maybe you expect the result of capturing through a Red filter to be a Red coloured image? Nope you still get a greyscale image no matter what filter you use. The colourspace is usually also set to be greyscale in the saved image. You need to convert the image to RGB colourspace then work on each channel by copying your filtered greyscale images to the appropriate colour channel. So the Red filtered images you combined and stacked to produce a grey image gets copied to the red channel of a blank image, the green filtered to the green channel, blue to blue. then this image will become full colour. There are different types of colourspaces and different ways to combine your filtered captures into an RGB file of some sort (ie colour). look into tutorials on doing this for the software you have.
So good news your captures are great, keep them safe, now just work out how to combine them
and yes you can mix and match any of the filtered captures into any colour channel to get funky colour results start with getting your red green and blue captures copied into those channels of a single file first and go from there.
