Thanks for all the suggestions guys!
Pooh, the disturbing thing is that she may actually go for those ideas.
Ok, I've been sent a link to a site specializing in custom MLPs. Here's what she suggested - RIT dye (whatever that is) for the body and hair. You mix it up in a bowl of water big enough to dunk the pony in. Don't know how you'd do the hair without doing the body & vice versa. She said acrylics for the eyes and traditional bum decorations, then put sealer over it. She said "NO!" to the permanent markers. I guess sometimes they bleed as they're drawn on, so instead of the straight line you wanted you get a feathery line.
I have to admit I'm torn. I want her to be happy with the results and I want it to be as easy as possible for her, but dye sounds dangerous. These are not going up on a shelf to be displayed, they will get played with - A LOT! So I'm not expecting the artwork to hold up well.
What do you think?