First off, I not new to asp.net but I'm not familiar with the new MVC stuff but from what I've read it seems to be a step in a better direction.
The current code is all in one big dll. The application code is divided into multiple folders representing the different departments and each department has it's own pages for handling general stuff like employee management, reports, budget and also their own information. For example, even though each department uses a different webpage for employee information handling, they want different fields and so it was simpler to create different pages than to use a single page that adapts to each department. But it is really a nightmare to maintain right now and I would like to create a parallel project where I could start a fresh project, create a better structure and from there start migrating the old code to this new environment and refactor it as I go.
The idea is to migrate the old application to a new web site that has a similar look while maintaining both operating until everything is running in the new site.
It may sound insane but it really is used extensively for hundreds of people everyday and it bugs me that I have to modify crappy code to make it work.
How would you go about this issue?
 If found this link Things You Should Never Do on another post, very much to the point of my question.