As for organizing files, color coding helps me. Everything to do with this scenario is blue, everything with this one is red, etc. Alternatively, start every file name with a letter that will keep it alphabetized with like files. “B filename1” “B filename 2” etc. Subfolders can also help, but can also get confusing if you forget where each file is located.
But like @Moonbeam said, what will probably help most is being able to go into your lab each day and interact with other humans face to face.
I know some grad programs are very competitive, and others are very cooperative. Which style is yours? When my friend was getting his doctorate in…something to do with chemistry, he felt very isolated because his peers were very backstabby and he was used to a friendly cooperative environment.
I will say once again. I think you can do it. I think you’ll have that Master’s if you want it. But you don’t have to. Starting salary for someone with a nuclear engineering degree who wants to work at a power plant is like 100-130k. You can already have a very successful career with the degree you have.