The short answer is that you need to turn the measurement into a linear measurement parallel to the canopy rail... To do that, you'd be doing a lot of trigonometry to work out you CG location, and every time you make one of those calculations you risk making an error. You also need to know your exact mechanical dimensions more accurately, as small deviations from the "design ideal" could be magnified by each calculation.
My procedure for measuring tailwheels, which I have used on a large number of tailwheel aircraft including my own:
1. Weigh the entire plane in 3-point attitude. This is your empty weight, and is independent of attitude.
2. Raise the tail until the plane is level, and read the weights on the two main gear. Don't bother trying to weigh the tail.
3. Add the two main gear weights from (2), and subtract that total from the empty weight (from 1). This gives you the weight on the tail when level.
You now have the weights on the mains, the weight on the tail, and the empty weight. My personal opinion is that using the "book values" for the locations of your main gear and tailwheel will be just fine, provided you have built the plane nominally to the plans. Even if you've used different-sized wheels, the axles will still be in the same places when the plane is level.