Hi Jim,
I certainly don't know enough to tell you what to do, but will instead offer some food for thought.
On the Brothers website they show a series of photos on replacing the cab corner. Instead of installing a new inner panel they cap the hole inside the cab and weld on a brace underneath. On my truck the inners were in decent shape so I just replaced the outers without facing the question you have before you.
Here is a link to the Brothers DIY articles.
http://www.brotherstrucks.com/techarticles.asp
