Ok guys, guess I'm gonna have to dive deeper into this. Here's my exact scenario:
In maya, the object that I'm exporting is not centered in the scene, so it does have some translational values. I'm exporting it as an obj, should it be at the origin with the translates zerod out? Export the chan file from the camera.
Nuke: Import the obj, into Scene>Object>objReader. Connect it to a scene with a new camera. In the camera dialog, import the chan file and enter the horiz and vert ap sizes after converting them from inches to mm. Grab a scanline render from the scene and merge that over the maya rendered plate. I've switched the rotation order and xyz seems to be the closest match.
I'm quite confused why they don't line up, what am I missing?