What color did it change from and to?
Did it come on suddenly?
Is she eating and drinking and pottying normally for you?
Does she have raised lumps in her skin under the spots?
Did she have any treats just before this?
Fur changes can go along with intestinal worm infection, skin problems such as hives (the lumps I was asking about) or skin infection. In some dogs irritation from parasite bites such as fleas can cause a coat color change.
If you live where insects are active this time of year insect bites or stings can also cause coat changes because of trauma to the skin.
If she seems to be shedding that is another possibility. The darker color may be where the new fur has come in and the lighter color be the old dead coat. It may be the diet change has caused a coat change too or hurried along the change over of the coat for spring.
Crying can be due to pain, itching, stress etc and it is hard to say which the problem is or where the problem is located.
If your dog might have gotten into anything toxic, appears dehydrated (see if a pinch of skin over the shoulder blade stays stuck in a tent form or flows back down normally when released), has a rectal temp over 103.5F (normal is 100.5-102.5F), has gums or tongue that look white, blue, gray or yellow tinted where they are normally pink, has a slow color refill if you press on a pink area of gum or tongue, or is becoming lethargic and non responsive to you then you may want to get the dog in to see a vet today if possible.
If she is itching you might want to see if some plain Benadryl helps with that. A usual dose is 1mg per pound of dog every 12 hours. If you choose to use that please read here about cautions
Hope this helps you!