Hi Jenn
There are many things that could be the cause of your son's difficulty in class, from medical reasons to social/emotional. Since its still early in the school year, he may be still be having trouble with the whole pace of a classroom. Preschool and Day Care are busy places with many opportunities to move around, choose activities, rest and be playful. Not a lot of "authority" or rules as compared with school. In school, there's more structured activities that require a child to sit more and focus on the task without wandering around. Its a big change to an active boy, to have to sit still, listen, and focus on things he may or may not think is all that interesting. Its also difficult for a child that is used to a slower paced preschool/daycare...school is fast paced with lots of waiting/listening and many children, teachers and staff to learn. If he has an attention deficit issue, he'll be even more unable to transition to a classroom setting.
I would chat more with the teacher and find out where she thinks its the hardest for him to focus. I would also try to set up a behavior plan with the teacher and even the principal (sometimes the authority of a principal can really make things hit-home with students, LOL!) where he can earn stamps/stickers on a chart for each activity that he's able to sit through and complete throughout the day. At the end of the week, you can decide what he's earned for his prize (a trip with you to a playground, buying a new book to read together etc). Coming in for a whole day and witnessing him in-class might be a good idea as well...if he's able to keep it together while you're there, you'll know he's not medically unable to sit/listen/complete tasks. You'll also gain better insight of his day and what he faces for changes/stimuli/activities.
The teacher unfortunately cannot restructure her curriculum, so if he's bored, he'll need to learn how to cope with those times and get his work done. Kindergarten isn't boring and is usually a fun little place to be, when you're not in trouble, lol!! She can keep his issue in mind and allow him to walk around a bit etc., but unless he's showing signs of absolute genius, he cannot possibly need a special curriculum for a "bored" student. He may simply be overstimulated with all the new-ness of school, new teachers, new kids etc. and is trying to "get away" from it all by being a clown and taking extended trips to the bathroom. Headaches and tummy aches that aren't real, tend to be stress related and something that he may need to talk out with you or a school counselor.
Putting him on medication for hyperactivity should only be pursued once you've tried all the other avenues (I think his teacher is suggesting that in saying he needs to see a doctor, since doctors aren't going to help with schoolwork, LOL!!). He may have an emotional issue that needs to be dealt with instead of a hyperactivity issue (especially since you've said he has had outbursts before). He may be overstimulated right now with all the changes, all the new authority and especially the structure, that he will grow out of the more comfortable he is, or it may get worse as he gets behind in work. Whatever the reason, try all avenues first and especially spend lots of time with him, chatting, playing and engaging in time alone with you. Its hard to be 5, start school, and even harder when you're in trouble...he's trying to find his way and you're not a worrier for being afraid for him...you're a good mom.
Good Luck with it all,
Jen