I have some footage shot on the jaunt for 360. So I end up with a stereo latlong image. I would like to use octane render for nuke to position the camera precisely and line up the stereo imagery.
Isn't this as simple as just having the camera point to the origin of the scene - so it is pointed to the mirror ball you took the footage from? (perhaps I am not understanding well enough what you are trying to do). Is this for a still or animation? If it's an animation, you will need to edit the Octane scene in the plugin an use the IBL images as an image sequence for the Texture Environment.
I am also using the footage as a source for the texture environment and reflections, so I want to be able to also animate the sun position in Nuke and line it up.
I don't think Nuke is the package to use if you want to do this. The sun direction is animatable - however it would be tricky - because you'd need to work out the sun vector each frame which would not be trivial. I would recommend instead using something like Modo to animate the sun (by animating the directional light used as the sun) and then exporting the animation to ORBX, which you can load in the Nuke plugin.