First, I cannot picture out how it can take 15 minutes to copy something from A to B in GIMP, this is very unlikely, it should take few seconds big max
Can you take a full screenshot of GIMP with chart A and chart B with the Layers dialog/stack in the screenshot (or reproduce 2 tiny charts of 4 images each opened at the same time in GIMP, if information's of your charts are not meant to be seen by us), I need to visualize what you've tried to explain.
Can you take a full screenshot of GIMP with chart A and chart B with the Layers dialog/stack in the screenshot (or reproduce 2 tiny charts of 4 images each opened at the same time in GIMP, if information's of your charts are not meant to be seen by us), I need to visualize what you've tried to explain.