Python program to Website Application
If the application needs to talk to a database that already exists, then django won't buy you much value IMO. since the admin interface won't work for that part unless the db schema adheres to what django expects (auto increment int primary keys etc...), the same goes for any other webframework that presumes an expected schema.
So then, sqlalchemy is your best bet. It has an orm layer, but you don't have to use it, you can get a lot of bang for the buck just using the query interfaces. 
So as far as webframeworks go, that narrows it down to anything that can use sqlalchemy. Which is anything but Django, Zope and probably web2py due to the reasons mentioned above. Though for Zope it's value is somewhat derived from the fact that it's backed by zodb. But zodb is not going to help you at all with your existing database and data.
So out of what is left of the web frameworks, what I would use a selection criteria is what it's abilities are for routing requests to views. And how well it matches your url generation strategy. IMO, pyramid is very flexible in this area. But you might not need that. You may be able to get by with flask or bottle. Or even straight webob. 
Another slightly less important criteria is template engine/language, most frameworks will support the more popular ones, such as jinja2 etc... 
My personal choice is pyramid because it scales nicely from super easy to super hairy in the request routing department. But again, depending on how you want your urls to work, you may not need that.
I'm working on a project which is converting a 50mb python Graduated interval recall rating system for pictures and text program to a website based application. (and then design a website around it) It needs to connect to a database to store user information frequently so it needs to be run server side correct? Assuming I know nothing, what is the best structure to complete this?  There seem like many different options and I feel lost.
I've been using CGI to create a web UI for the original python code.  Is this even possible to implement?
What about
pyramid / uWSGI / pylon / flask
or Django? (although I was told to refrain from it for this project)