I think Ultron will be a sort of software that makes its rounds through shield and HYDRA, and it gets upgraded with the same software that JARVIS is. I think that we'll eventually find out in ant man that the program that made its rounds was originally created by Pym, and Howard Stark, and that JARVIS is a branch of that original software. The original software makes its rounds, and reconnects with the JARVIS type stuff, and Tony builds him his bodies.
I don't think Tony built Jarvis. Look at his other robots. Dummy. That is some sort of responding AI, or atleast an AI runs it. He can build a super advanced AI in JARVIS, but he can't create decent software in "Dummy"? I don't buy that. I think JARVIS was once real, and he died, and Howard Stark, was able to put his brain patterns in an AI, which was something developed off of what Howard, and Pym originally did