When going from the original color to the desired color I'll just directly follow the amount/feeding order from that site and cross my fingers. If it doesn't get the desired result, I recalculate using the same site from the current color to the desired color. After recalculating I'll write down the new feeding order and feed the chocobo until the message pops up that the feathers are changing, at which point I wait out the color change. If the result isn't what was desired, I continue down the feeding list, waiting out each color change as the message pops up that new feathers are growing in.

I just used this method again on an alt that didn't reach the desired color the first time, the new calculation had about 8 fruits to go through, but I got the feathers message with the first fruit and stopped at that. That one fruit managed to get to the correct color. If I had just thrown the entire second batch of fruit, I would have overshot the desired result. Whatever method you use, good luck!