I am sorry to say that absolutely you should have tracked in mocha without converting the image to a line drawing. Because mocha is a planar tracker, it really needs the texture of the image in order to get a rock solid track. Also, you will want to track with your grid and surface tool on, so that you can see whether or not the tracking data is incorrect. Your roto shapes in mocha will only follow the tracks, so if the track is not good, your roto shape won't be easy to manage either. Don't trust the splines, the splines all only follow the tracks and as they animate, they do not change the tracking data.
I would suggest that you retrack/re-roto using the original footage. In general, you want to do any effects like "line drawings" or color corrections after you have done your roto and VFX work on a shot.
Please let me know if you have any more questions and I will be happy to help.