Your technique will not create the best results. Generally, Zenith replacements are more suited to clone & patch technique (does not require Mocha) because the is not much planar data to track on sky. To get a good Mocha remove, you need to have a good solid planar track on the background (in this case the clouds). If I was doing this job, I would create a simple patch offset in AE or Premiere with a some feathered masks on either side of the patch area. You could use Mocha’s Lens module to help here or the built on Adobe VR tools to flatten the Zenith view>do comp>undistort back to 360. Look up Mocha VR “lens workflow” for this.
If you really wanted to use Mocha for this tasks, you should display the zenith view and try to track the clouds just below the black hole. Since the black spot does not move, you need to avoid it to get a track on the movement of the cloud pixels. Once this is tracked, then use the UBER KEY and make the shape layer cover the black hole. Might need 2 keyframes. Last step is to make a 2nd mask layer around the patch hole. Without following this type of technique, the remove module will not work on shots like this.
Another options is to again flatten the zenith view in AE, precomp, then use the new Adobe Content Aware Fill tool.
Best of luck and hope this helps.