Do you have to go to work? Could you possibly spend some or all of the day "helping" at his school? Sometimes I have seen this (from a teaching viewpoint) and have found that little people just need mum about a bit more for a day or so. You don't need to be in his pocket but perhaps help out in the classroom and possibly do some organised games at lunch or help out in the canteen. It would give you a chance to assess for yourself how school is really going and perhaps give him some confidence to face school as well.

I totally agree with the conversation thing too. I suggest trying "I bet it's really awful having such a sore tummy. Can you tell me exactly what it feels like?
Do you know why you have a tummy ache? have you been eating different things?
If you can when he doesn't have a sore tummy ask him why he thinks his tummy doesn't hurt now.
Sometimes little people will tell you whats really going on if you ask the right way. Sort of let them do their own problem solving.
Keep in mind noone ever wants a sore tummy so trying to solve the problem together might work.
I wish you all the luck in the world and really hope it's not something serious.
Oh and by the way I did have a bout of this with a group of girls in a class once. One of them had real stomach problems and had a lot of time off school and hospital visits and several of her friends had sympathetic pain. I do believe they really did have sore tummies but I think it was in sympathy with their friend. Once she was sorted the problem of tummy aches seemed to go away!