We are in the process of migrating an IE application to Firefox. Do you recommend a tool that can automate to a certain extent this process. Perhaps this tool could help us identify code that is browser specific. Do you see this as possible?
Unfortunately there is no such tool focused on the migration of web applications to different browsers.
I suggest that you start by using a reset stylesheet.
A reset stylesheet will reduce browser inconsistencies like default line heights, margins and font sizes of headings. The reset stylesheet will not solve your problem, but at least it will help you avoiding the situation where you be will fixing your layout for the other browsers but to break it in IE.
There is no way to automate this task.
Introducing a reset stylesheet may be a good idea (I don't have much experience with them) but may require a lot of re-working on the IE end as well. I can't say how much.
Reset or not, the best thing to do is to set up Firefox with Firebug and Web Developer Toolbar, IETester, and IE 8 with its developer console. Grab a big cup of coffee and start working systematically through the aberrations. From experience, 80% of the problems are based on a very small number of CSS settings and will probably go away quickly. The other 20% will be the ones you might need the coffee for.
Make sure you establish browser specific style sheet files using conditional comments from the start.
There is no tool as far as I know. If you're using any ActiveX components you will probably have a lot of work on your hands. If you're only having to re-style then you'll need to factor in what IE versions you're supporting at the moment. If you're using seperate stylesheets for IE6, 7 and 8 (or some combination) then you can normally seperate IE6 into 1 stylesheet and the other browsers into another stylesheet.
One of the key things to look at is the way the box model is different between IE and the rest of the browsers out there.
If your application dosen't use CSS stylesheets then your in for some major headaches.
Really need more details to give you a more accurate diagnosis. What html elements does it use, does it use CSS, JavaScript, etc?
Edit: missed your tag for JavaScript - look at the different ways that browsers handle whitespace with JavaScript: Firefox and Whitespace
A lot of people have recommended a reset stylesheet, however, I'd recommend you actually create your OWN reset-stylesheet and seed it explicitly with the defaults from IE. This will be redundant for IE, since it will default to those styles anyways, but is critical if you don't want to have to rework both your current IE implementation in addition to Firefox.
There's a link to a grid with IE default style settings here:
http://stackoverflow.com/questions/214378/how-can-i-locate-the-default-style-sheet-for-a-browser