Trouble getting hemi running right

One thing to note on fuel pressure is that I believe the Megasquirt system wants a manifold vacuum referenced regulator. What that does is assure that the fuel pressure relative to the intake pressure is always constant, so you have a known amount of fuel. Say for instance you had a boosted engine running 10 psi manifold pressure. If you have a fuel rail pressure of 60 psi, when the injectors open they are only seeing a 50 psi different, so what you think you are getting for flow at 60 psi is not what you're actually getting. Manifold referenced regulators adjust relative to that. That being said, I would expect to see the rail pressure drop from 58 at idle, not increase, at least assuming you're running NA.

As for the other issues, I ran my system fine with open headers, but it was still on a rough tune. It sounds like you're having some kind of sensor issue. I would try doing a data log of all of your sensors through the Megasquirt and watch the traces to see what it's doing. If you are seeing huge spikes in the O2 or injector duty cycles it might point to an exhaust issue. It seems more like a "accel pump" issue to me at first impression though. You might consider posting on the Megasquirt forums with your data trace. They are usually pretty good about giving feedback.