I do have a decent MIG welder, and a flanging tool, along with most any other tools I'll need.
Most guys would say throw the flanging tool away, or at least bury it in the bottom of the toolbox. If you use it, you're building in a spot for the rust to take hold again.
Here's a good resource for metal working:
MP&C Shop ProjectsMP&C (Robert) hangs out here every now and then and is a metal working artist. If you read through that thread, you'll get lots of good advice. If you have a specific question, I'm sure that Robert wouldn't mind you sending him a PM. He has some good advice on welder setup and how to do a good butt weld on sheet metal.
Good on you for tackling the project you have.

I'm in the process of replacing rockers and cowls on my cab and would be happy to share my experiences with you.
I agree with everything that Bartamos said in his post. Good points.
If you can, you might consider putting the cab on a rotisserie. I built my own and it's making things a lot easier on the old body (mine

).
Here's some pics of my setup.
Rotisserie