The canon colors are red, rose, golden yellow, and pink. And if you want to be picky, new members start with russet reds and browns and work they way up through dark reds and mustard yellows, to the brighter colors of the higher clergy.
So if someone can go through the pallete and re-tint the blueprints than save it throughout the module this will fix it a great deal:

Father Richart in the properly colored temple next to a properly colored armor set.

A standard guard next to a properly colored armor set.