This is what I got with:
1. LinearFit, using Ha as the reference image
2. Combine with ChannelCombination SII -> R, Ha ->G, OIII ->B
3. Adjust STF sliders then transfer STF settings to HistogramTransformation.
4. Finally tweak HistogramTransformation to line up the red, green and blue peaks and raise the black point.
I'm not sure of the cause, but there are lots of dark spots on the greyscale images, which end up as colour splotches on the colour combination.