A sudden change in food can cause digestive upset that will make a cat uncomfortable.
However, runny eyes may indicate an upper respiratory infection. You can read about those in cats here
http://www.marvistavet.com/html/feline_upper_respiratory.html
Cats really don't need milk once their mother weans them and it can even cause loose stools in many kittens after weaning.
A weaned kitten can do fine with dry food, canned food, and plenty of fresh water.
If the kitten has not seen a vet you should consider seeing one to make sure she is clear of internal parasites such as worms, external parasites such as fleas and gets treatment for any upper respiratory infection she might have.
Hope this helps you!
Cat Health, Behavior, Care Expert
30+ years cat owner, rescue, breeding, study of behavior & health care