Whit,

You're right; to find the balance point with a Vanessa rig you need the plane level, just as you need it level when balancing it on your thumbs. (We talk a lot about finding the CG, but we don't need to do that and we never do in practice.) It is true that the plumb bob on a Vanessa rig always points to the center of gravity, but knowing that doesn't tell you the balance point unless the plane is level because you don't know where on the imaginary line down the string through your fuselage the CG is. Your pictures showing the "wrong CG" aren't really showing the wrong CG, they're not showing the balance point at all. Unless the CG is a lot higher than it normally is (i.e., unless it is on the very top of your fuselage), the point on the top of a tilted fuselage on a Vanessa rig is not the balance point. All you know on a tilted airplane is that the balance point is somewhere on a line running diagonally (in a fore-and-aft sense) through the fuselage, and you need to know more than that. The balance point will be somewhere ahead of or behind the point on top of the fuse, depending on which way it's tilted.

What you are doing makes perfect sense to me.