Also, he has probably gotten out of the "routine" of going to school. Once he gets back into that routine, it will be easier. Make sure if he stays home because he is sick, he stays in bed and doesn't have too much fun.
funny about lunch time. You might ask his teacher what typically happens then. Do they all go to a big lunch room with other kids for example? Maybe the teacher could find a 'friend' that he could eat lunch with. If he doesn't eat lunch at home, its ok to just give him a light snack. cheese and crackers, cookies, a fruit drink, etc.
Well, vitamins can help. Is he getting enough sleep, perhaps an earlier bed time by a half hour. Not done in a punative way, but in a "we need to get our sleep" kind of way.
Lots of kids have a really hard time transitioning into kindergarten let alone all day kindergarten. By the way, do they have a half day program there? He might do better with that.
And new school enviroments are notorious for kids getting sick. Mine always are sick in the fall.
Do you think he may have some anxiety? I would watch this as that can make life very difficult and can be treated. Good luck