Exclude certain items from certain shipping methods?

I have some larger items, but I can only seem to get them to ship via priority flat rate, which they will not fit in. Is there a way to exclude certain shipping methods?

I'm not sure about this one, I would try experimenting with different shipping properties when you edit an individual product. Otherwise maybe try changing the weight limits, etc on an individual shipping method.

Are you using Professional or Ultimate? You could use the Suppliers function which easily does this in Professional, unfortunately for Ultimate, you'll have to wait for 3.1.1 as they removed Suppliers feature from Ultimate but not Professional.