I actually was able to get it working. The MM save file I had downloaded didn't work directly. I loaded into that file, then created a new MM game from it. Then I did the 4 shrines so i had my runes and amiibo ready. Turned amiibo support on and saved the file. Then I copied my Normal save to folders 6 and 7, overwriting the old game_data.sav files. I reloaded Cemu, loaded into the save, and voila! My old save but now on Master Mode!
And yea, everything works great except for the Hero's Path. It shows the path from the old MM file. So unfortunately it won't help me find out where I've not visited, but I think its an OK trade off.
For those that want it, here's the MM save file I used (right after doing the 4 shrines).
Make sure you enable Amiibo in the Options before saving!!! (or it won't work in your new MM save)
I am using BOTW version 1.4 (although I think it still works for 1.41) with Cemu 1.11.3
Hope this helps!
Oh and JoycieC, did you ever find a way to get the Hero Path data over as well?