Have you tried importing the panorama images into Lightroom? In LR, you can select capture order to sort the images, and also rename them, appending a leading or trailing incrementing sequence number in the current capture order, to the original file name, to do exactly what you are describing. You can also stack images by capture time, and set the
time interval of each stack grouping. The panorama sequences will be tightly grouped in time, vs. your manually shot images. If you specify say a 10 second interval between stacks, your first panorama images should then be in a stack, to help spot them, unless all your other images are 3 or 5 simultaneous shots. LR's ability to organize your images is limited only by your imagination to get the results you want.
Lots of magical lighting scenarios don't capture well digitally. Our eyes have a far greater dynamic range than any camera. Try different stitching programs. They all have slightly different algorithms. Some are better than others, depending upon your scene. Also several of the stitching programs allow you to manually override the automated stitching process to correct for errors. Learning about control points will help, too. Happy stitching, and have fun !