This brings back memories. I did the same with my own alchemy books some ages ago.
As bhl said, the Font Color setting is what you were searching for. It's best to divide the six numbers into three pairs in your mind. The first pair is the red color, the second green and the third blue. If you want simple red, green or blue inks, you just need to do something like this:
Black - 000000
Dark red - 500000
Dark green - 005000
Dark blue - 000050
Bright red - 990000
Bright green - 009900
Bright blue - 000099
If you want more extravagant colors (like brown for aged ink) then you can find out the exact numbers for them in the CS. Go to the World / Interior Cells menu, choose the ToddTest cell in the drop down menu (so that nothing happens, even if you mess up something there) and then Select Color. This way you can choose nearly ANY kind of color you want. Just don't forget, that the highest number for one of the basic colors is 99 and that too light or bright colors may end up completely illegible. And always test it in the game.
As much as I know, setting more colors in one line of text does not work.
The game will choose only one of the colors (in my experience it was the last one used on the line). On the other hand, you can have every line set up in a different color - just add the
(replace the zeros with your own color) on the start of the line. Also remember, that all the text below such a color change will be affected by it, so you HAVE to set up a new color, if you don't want to leave it that way.
Btw, you may wish to split the alchemy into more books, rather then have a single long one (is what I did, split them thematically into four books - restore / cure; fortify; resist; traveler's - aka all the feather, light and so on). After all, you can choose freely, how heavy the books will be, thus shouldn't become less handy for the player (carrying four 3 kg books would be a real hell, lol) and will be more well-arranged. Of course, it is up to you to choose, how your book will look like in the end. Good luck with your project.