Andrew,
I am not a welder.
However, my opinion is you can replace just the rotted out section and still maintain structural integrity if you weld in some sheet under the good channel and the replacement channel. You might be able to bend some 1/16 or have someone do some for you to get just the u shape to tack under and to the two pieces and bridge them if you get my meaning.
Just be aware that some of those channels contain wood used by Willys to help with rigidity 70 years ago, and that contributed to the pieces rotting out. There is also wood inside the channel at the right rear quarter panel where the four holes are behind the rear wheel. That is where the spare is mounted on the civvy version and they used the same sheet metal. Many jeeps are rotted behind there as well.
I say that to caution you to make sure and get all of that rotten wood out or you'll just be in the same place in another 70 years or so (snicker).
Several folks have documented replacing sheet and channel like you are doing.
Patrick did some pretty heroic sheet metal repair as well as frame work:
http://52m38.blogspot.com/search?update ... date=false
Brett has done some as well:
http://s1201.photobucket.com/user/1bral ... t=3&page=1
Both have project pages here as do many others.
Thanks for the photos. Please post more. We learn from everyone.
And that you for your service.
Brian