Here is a post I made when I completely cut out my rocker panels and welded in new ones.
I have minimal body work skills, and even less mig welding skills. But like you, I am always up for a challenge.
It's not the same as what you need to do, but maybe it will give you some courage to tackle the job.
Any time you don't cut out all of the rust, you are just buying time till it comes back even worse than before.