hi A.! my first question is... did you take time to introduce whole milk to him before u switched him completely? it could be that it was something new and different so of course he enjoyed it, but now hes ready for his formula, so therefore isnt drinking anything in protest. my son who is now 19 months old has a milk protein defeciency which means that he breaks out with milk products, not just milk. at first, we would give him a teaspoon to a tablespoon here and there and that amount was ok but when we switched him over, he broke out. maybe ur son isnt having visible reactions to the milk but it could be upsetting his stomach. i suggest soy formula or soy milk and even goats milk. it is much easier on the stomach.
as far as reactions to teething... we have asked our pediatrician about teething and she has said that running a fever is not a symptom. u get a fever from an infection of some sort, ie... ear infections, flu, cold, etc. those symptoms that u did describe could be from his shots. those are classic signs of his body reacting to them.
my only suggestion would be a vaporizer, they have the safe ones now for children that dont require any medicine in the vapors to help clear up the congestion and runny nose. also, having him play in the bathroom with a hot shower or bath running could help break the congestion as well. i hope ive helped some and i wish u all my best!
K.