An update, actually two, on the Rogue Jupiter simulation.
The two files posted are at 54821 and 56178 simulated years, or somewhat 20,000 years after the rogue planet was ejected and 4,000-5500 years after the last update. As you may recall, in my last update, I thought that the system was becoming stable, but it appears that I was wrong.
In the 4,000 simulated years, roughly 380 orbits of Jupiter, between the last update and the earlier file loaded, the outer solar system has stayed more or less stable, The Kuiper Belt continues to very slowly evolve due to the disruptive effects of both Uranus and Neptune, but that is VERY slow. The big effects are in the inner solar system. The Earth and Mercury, still in the strange nearly perpendicular but apparently stable orbits, are more or less unchanged. Jupiter, however, has moved much closer to the sun and Perihelion and has forced both Venus and Mars into much more elliptical orbits. There is also what appears to be a possibility of a close interaction between Jupiter and Venus. It doesn't look like Venus and Mars can interact too closely give that their orbits are also very inclined to each other.
The next update, only about 1350 simulated years later, shows rapid evolution of the inner solar system. Jupiter's perihelion is still slowly migrating closer to the sun and Venus now has a very elongated orbit that is passing inside the orbit of the Earth (previously the closest planet to the Sun). In addition, it appears that the evolved orbit of Jupiter is set up so that it will regularly interact with Mercury.
I was planning on stopping this simulation in about another 4,000 simulated years, and still might, but I'll probably keep running it until this set of interactions has worked itself out.