I'm repeating this from the last thread, because even if THIS theory doesn't work, I think we can build upon it...
While I have no new crystal, no new lights, can't even find a spike trap, I do have a theory...
When the 2nd crystal goes into the mini city, it is actually sitting on top of the original crystal. Since they are glass, the original colors show through. Note that hte blanks match up, as does many of the primary colors. So, any colors that remain the same won't change (duh) and any new colors need to be blended to achieve that result. As such, I suggest you only read the scrolls you need to read to obtain the blended colors.
I know it doesn't make much sense. Here's a layout I worked on...
So you only need to read 8 new scrolls to achieve the lighting effect of your new pattern. Make sense? Someone checked out one of the existing colors and when he went into a room there was more than one of the scrolls there, that was a flag that maybe the colors that haven't changed should be ignored.
also, while there is NO confirmation on this point, I would suggest reading from the color catalogs in the same order as the dots from the original crystal.
Since I can't play, let me know how it goes.