Great looking wagon!
On the fender well rust issue, I have written many times about this very thing. The most common mistake that people make is to attack the problem based only on what bubbles or holes they see from the outside. By the way, the foam didn't create the gap. Wagons were designed with that gap. And because of that gap between the inner fender well, inner well skin, and outer skin (body) it is a wide open trap for dust, dirt, and moisture. And that leads to a serious rust issue that cannot be fixed correctly from the outside.
You and others who have replied are correct. The previous owner probably cut out what he could see then used body filler. It never works long term. The cancer is coming from inside. So the only way to fix it right is to either remove the outer quarter or the inner well to get access to all of it. I agree that if the body is straight other than the rust, I would attack it by removing the inner well or inner skin. The inner skins are available new. And the new quarters are so poorly made that it's very much worth the effort to save the original body where possible.
And if you remove the inner well, you can redo it much better by making a removable or permanent cover over the catch-all "V" notch.
I think you have a gem there and I hope you enjoy the wonderful journey of putting another Willys wagon back on the road. It's a truly enjoyable thing to do.
Here is a perfect example of the issue. My wagon didn't look bad at all from the outside. Just a few holes and bubbles around the fenders. Just like yours.
But here is what it looked like on the back side. This is the inner skin I was talking about. This arched piece is available new from many vendors. And it's a nicely made piece.
Here is a photo of a new one from Kaiser Willys for example. Walcks Four Wheel Drive also carries it. And others as well.
Here is the link:
http://www.kaiserwillys.com/product/176 ... ccessories
You may already have this info, but just in case.
Here is the back side of the quarter after it was removed.
This is what the "V" notch looks like when it's taken apart. If I hadn't gained access to this inner section, it would have been a total waste of time. Yours may not be as bad as mine was, but it's worth it to find out. You can get to this from the inside though. Even after I replaced all these parts including the entire floor, I took my entire wagon to Oregon to have it dipped in acid to kill all the remaining hidden rust. After that, it was dipped in phosphorous. Totally worth it IMO.
Hope this helps.
MB