Hi Leanna,
I understand that it’s been a while that we are in a back and forth and you and we were unable to find the problem on your specific case.
I am really not sure why this is happening on your installation. We have many other installations that do not have such a problem. Maybe the conversion you said from X to Pro did not work well. I am not sure.
The important thing to rule out is the server related problem possibilities, not only the timeout but the mod_security rules and other environmental factors.
I suggest that you move your website to another server or your local machine and check the case. That way at least we will make sure that the problem is not server related.
If the problem is not that, then it might be a problem of the database as you say some pages work and some not. I have never encountered such an issue. The only thing that comes to my mind is to clear the database transient cache that might help. For that, you will need to install this plugin.
Thank you.