Well I have a bunch of big panoramas and I normally use Hugin to process them. But it seems to have trouble on El Capitan and also apparently you know need to install a separate tool called autopano-sift-c to get control points to work properly but this didn't seem to really help.
I do find Hugin pretty obscure, but after using it a bit, here are the key learnings:

• The is a Panorama and a Fast Panorama Window. The names are very similar but the functions different. Fast Panorama has the simple load and align commands whereas the Panorama has the controls that let you straighten an image (I have no idea how it does that)

• Also Fast Panorama when you create doesn't seem to have the right parameters. Use Panorama's stitch and make sure to click on the crop as this seems to give abouit 30% more pixels to the image.

• Also create it with both fused and blended as well as from an stack and blend. This seems to use two different algorithms with the blend looking more natural as it seems to correct for exposure differences (even when I lock exposure this is a problem you really need the camera to be in full manual and set locked white balance, but I get lazy and forget, so the software tries to correct). Otherwise the sky can look very wierd as the color shifts.

• I normally create in TIFF to get the full 16 bits that the raw image has, but you need a big disk. For a 20 megapixel image a single TIFF is 125MB and stitched images are often 200-400MB. It is a shame to get rid of all that resolution with a 8-bit jpeg.