I am facing a similar problem, where I have to move around 8000 posts from one category to another. The script is timing out immediately.
I don’t really want to make any changes to the server configuration as I don’t feel comfortable doing it but don’t have a problem having to do an operation using the plugin multiple times.
Hence, I would like to suggest adding an option to limit the number of posts that are being moved by the plugin. If I had an option like that, I would be happy moving 1000 posts at a time, something that my server seems like it can handle.