I'm not sure that the workflow is the issue, here.
The Sigma 8mm circular fisheye is simply optically limited--it's a very extreme lens. Most professional VR photographers use other, sharper lenses, typically without as much coverage, and simply stitch the larger number of images to get higher resolution as well as better sharpness. Shooting full frame with a 15mm diagonal fisheye, or crop with a 10.5mm or 10mm, or even a rectilinear ultrawide, for example.
I've gotten my best 360x180 results with the Sigma 8mm with my 5DmkII, but even my little micro four-thirds with the Samyang 7.5 (full-frame equiv. of a 15mm diagonal) can sometimes beat it. You use the Sigma 8mm f/3.5 for the convenience of being able to handhold and cover the scene with four shots if you need it. But for ultimate image quality, even stopped down into the f/8 range and carefully manually focused, the loss of sharpness and the C/A at the corners of the image are something you're always going to have to fight.
One other thing to keep in mind is that
the Sigma 8mm's infinity focus mark on the barrel is completely inaccurate. You'll get best results by manual focusing with a magnified liveview. And then taping down your focus ring.