buscht I have not kept up completely with your project but I did notice you mentioned that when scroll sawing your parts that they did not fit back together. You also mention that in testing using a pen or felt tip that the program was correct. I am supposing here but in the actual cutting program did you compensate for the saw kerf? If not that will explain some of the not fitting. The fact that the blade is 1/4" (again assumed) you may not be getting correct cuts on radius uhor is that radiuses or radi, well whatever they are called the balde may be changing some of them!
Mike