Ok, a little update. I remembered that a .jmpprj file is formatted as a zip file. So I used 7zip to go in and edit the project.jsl file. It seems to just run how everything is opened and organized on startup. I deleted a bunch of statements in the script that all referenced "graph builder". I also deleted the statement having to do with the scripting index window, including some long series of letters and numbers that seemed to be a unique identifier for an instance of what I thought was the scripting index window. However, it may have been for the whole project, because when I opened the project, nothing opened *except* graph builder. However, this time, I could x-out of it. Then to test it, I just opened every file in the project, and now it's running smoothly.
I'll mark this as the solution for now, but once the customer service crew gets back to me, I'll probably add whatever they say as a solution as well.
Addendum: I also deleted a lot of temporary files that autosaved from script testing from the project using 7zip before opening it. I opened it after deleting, but before doing the above solution, and it still crapped out, so I don't think that did anything, but just for completeness for anyone in the future with the same issue.
Edward Hamer Chandler, Jr.