Example: I want to play as Switzerland. Their color is poop-brown. I want them to be blue like Sweden. I would do is go into 1492.inc and change wherever it says HEL to SWE and vice versa. Then go into text.csv and change the line that says SWE; Sweden; X; X; X;...to SWE; Switzerland; X; X; X;... Make a similar change for the HEL tag in text.csv. Then swap all the shield filenames with each other. Extremely tedious, but effective.
...and that would not be enough. You would also have to modify DiplomaticMatrix.csv, revolt.txt, ColonyNames.csv, ArmyNames.csv, RandomLeaders.csv and LandCosts.csv. Not to mention that you would have to switch the monarch and leader files. Not practically doable just to change colors.
/Doomie