Steve,
First off, you can't check how straight the fuselage is until you bring the fuselage sides into the top and bottom fuselage pieces. Try bringing all of the parts together and dry assembling the sides to the top and bottom of the fuselage. Use rubber bands to hold it all together down the entire length of the fuselage. This type of fuselage that uses interlocking parts actually count on all of the parts being together to be straight. It's the way it is designed. Taking the measurements like you are you won't be able to tell if it's straight or not. And if you go cutting the sides of the fuse now you will more than likely make things worse.

Ken