little horse- John is right, pretty much anything can be fixed if you have the time and patience. I've patched alot of those '40-'46 fenders, and most need patching in the runningboard area you are working on, or on the flange that bolts to the box side. Both of these are fairly easy places to patch as they are relatively flat, and both places are pretty hard to see clearly when the truck is assembled. The wheel opening is much more visible and therefore harder to patch nicely.
For the runningboard area, I usually trim the rust away and then start fitting a flat piece of sheetmetal in. You can bend the curve by hand. At the bottom, you will need to have a small 90* bend to give it strength. You won't be able to bend this without putting small relief cuts in the 90* flange to allow it to curve. If these cuts are placed every 1/4-1/2" apart, they can easily be welded up later. If the truck is somewhat together, the fender can be bolted to the box temporarily and the fender clamped to the runningboard to get the right curvature before final welding, and also to transfer the bolt hole locations. If you clamp the fender and board together when tacking the patch in place, the fender patch should fit good and shouldn't need much mud at all. If you don't fit the fender patch to the runningboard good, and the curvature is way off and you try to make up for it with mud, the bondo will want to crack when you bolt everything together. So take your time and get a decent fit before welding everything up solid.
