Confirmed on one of your previous imports that you can combine transparency (color struct) with specular lighting. Sweet! That's what the crystals need.
While doing so, I made an interesting discovery, if that's what you want to call it.
Let's go back to the Hyrule Castle import.
Remember how that stage had "broken" color nodes on the tent and a few side walls?
View attachment 109927
Well, Edwguard Flows made the tents/roofing have specular lighting.
View attachment 109928
If I enable the flags for specular lighting on the combo tent, it turns out like this:
View attachment 109929
SO MUCH BETTER! And I only added the lighting effect to the main green roof material, not the light green at the top, or the fencing, or the little jut out green piece before the lip on the entrance ways - so it can look even better.
So my "discovery" might be that all your "broken" color nodes in your imports, might just be that those materials had specular lighting enabled in the brawl file, meaning the color struct doesn't matter and could have been bad in the first place. I'm sure this is why some of your stages look too dark as well.
To enable specular lighting:
Bone struct flags contains (00010080)
Material struct flags contains (0000000C)
*I just updated my post from a few posts up for the specular lighting requirements to match these
For the above Hyrule example, the bone struct flags = 00150080 and material flag = 0000000C