Hi Kristy-
I know exactly what you mean!!!! Me and my son got flu shots, the nasal spray kind, and I felt sick in one way or another for almost a month. He was out of sorts for two weeks. I have a 4 month old so we did it to protect her, but I was so sorry I had done it. That doesn't mean that he isn't playing this situation like an accomplished pianist also. He's two and they can calculate. Try not to break too many old rules. Give him extras and special times if he's sick, but if its usually a sippy cup, then give him a sippy cup. Tell him your out of Capri Suns, you're really sorry, but all you have is the sippy. He'll take it. Or buy Honest Kids juice. Only 40% the sugar in a pouch with a straw like capri. A straw is a step up in development anyway, so ditch the sippys for some cool straw-no spill cups. By next year they may not allow sippies at your preschool so why not nip that in the bud now.
As far as the whining goes, I hate to break it to you, but welcome to toddlerhood. It never ends. I talk to the preschool Mom's and I have come to accept that my 2 year old's constant whining is just being two. Try not to battle too much. Its not worth it. If ever a saying fit a situation, "Don't sweat the small stuff" should be the motto of parents with toddlers. And the behavior can get catapulted by an event, such as being sick. Its like Helen Keller when she realized what the sign was for water. The light clicks on for them and they realize ....."Ahhhhh, I can manipulate. Cool. Time to be 2."
Also, get used to the frustration. Its a normal and healthy stage of development as children try to become independent. Ask him if he needs help, wait if he wants to try himself and then when he needs help, tell him to ask you calmly 'Mommy, can you help me, please" Eventually he will get it. My son asks for help about 50% of the time,sometimes he doesn't even whine anymore when he asks. Just keep reminding him that all he needs to do is ask for help when he's frustrated and can't do something himself. Also, explain to him what he's feeling IS frustration, what it feels like and how to handle it. He doesnt know what he's feeling is frustration. He's just pissed off.
But, honestly, I don't know your son. Only you really do.I would say if your gut is saying don't give him a second shot, then don't until you see a second doctor. Ask a friend, or if you feel comfortable, post your town for recommendations for a new dr.
It sounds like just a normal 2 year old, but you should get a second opinion. Don't get carried away with the panic over vaccines. The flu shot does cause flu like symptoms, but not feeling great and running a fever is NOT influenza. In the long run feeling crappy for a few weeks is a whole lot better than being near death if it really hits you hard.
Good luck and let me know how it turns out.