You can machine the gasket surfaces of the head and cylinder, including the cylinder base. You can (I believe) do multi-angle valve jobs provided that the grinding is limited to the valve seat itself. All engine parts must be stock, with no modification. Carb rejetting/EFI reprograming is allowed, exhaust system can be replaced, shocks can be replaced and fork springs, valving etc can be modified.
I believe the rules are on the AMA web site but I was too lazy to find the exact link.