I see, I missed that you are also experiencing a very slow system. Recall what I said earlier about running under high system load, if for some reason your computer is running at high usage rates, or running very low on resources, either of those can cause input problems, depending on your devices. I agree, it’s a good idea to look into why everything is slow, first, as the sticky shift thing might just be a symptom.
The slowdowns you are describing almost sound to me like your computer is running critically low on resources, rather than there being perhaps a problem with the project you are working on.
But before going to far into that, first make sure this isn’t just an issue with the project. Close the project, and use the File/New Project… menu command to create a new one, using the “Blank” starter. How does that one feel? What if you paste some text into it and type for a bit? Make a few documents and switch around. Now try loading the thesis project in parallel. Does the whole program immediately slow down? Or does just the main project window run slow, while the blank test project continues to run quickly?
Do a quick check of your hard drive free space as well. The symptoms you are describing sound a lot like a computer that doesn’t have much left to work with, in terms of drive space. A healthy system needs at least 15% of the drive left empty. You can check that by going to Finder and using the Go/Computer menu command. You’ll see “Network”, your main disk (usually with a silver icon), and anything else that is plugged in such as flash or external USB drives. Click on your main disk and use File/Get Info. Your usage status will be in the “General” section. Make sure “Used” does not exceed 85% of “Capacity”. I’d say anywhere between 15 and maybe 8 percent is where you would want to do some serious cleaning as soon as possible, but you shouldn’t see any major issues. Anything below 8% is entering the critical range—you could start experiencing data loss and overall instability, especially if it is run this way for an extended period of time without reboots. This would usually impact everything you do though, not just one program.
I would also check “CPU” usage that can be thought of as how much calculation the machine is doing at once. Again, from Finder, use the Go/Utilities menu command, and double-click on the Activity Monitor icon. Click on the CPU tab if necessary, and sort by “% CPU”. Is Scrivener using more than, say, 25% consistently? Is anything else using a 80% or more consistently? Web browsers are the big culprit here. Modern sites are festering with advertisements and such that can end up getting stuck, and continue running even after you’ve moved on to other pages. I try to restart my browser at least twice a day.