So when I try to run a file in PyWin, it opens an edit window instead. The first could times that it did this, I assumed it was due to some syntax errors in the file, but after I fixed them, it continued to open an edit window each time. This particular file has a lot of defined functions in it if that helps at all.
Does this problem occurred with every Python you run? Based on your problem description it is not certain if this problem is specific to the script you are trying to run or it is a general issue.
What I will do is that try running builtin demo script first to test & verify that you do have full set of libraries installed and runs fine. Once you verified demo script does run  as expected then you can look at your test file to see what is wrong. If you could not run demo script successfully then you would need to re-install PyWin completely to have it fully functional.
Trouble Running a File in PyWin