You're right, the forces at the chassis from the lower link are huge. The lower links do carry the majority of the load from the rear axle.
I will be honest and admit that this design I came up with for mount the lower links is far from the best option. Basically the ends of the two lower links have a long set screw running through them and the two threaded posts on the sides of the links are tightened against each other to put tension in the screw. The screw in the pictures actually bent, and since then I have removed most of the spacing between the link ends so that there is more support. Also, the aluminum link ends shown in the pics were replaced with some Jato rod ends. This will provide more flex in the lower links, which is good (especially since the links are steel and won't flex much at all).
As for fatigue on the chassis plates, TBH I think this is a non-issue. One of my concerns from the get-go was the potential for poor integration between chassis components - this sort of project has not been attempted by many, and thus there isn't much information on what works and what doesn't. So for this reason (among many) I chose polycarbonate to be the chassis material. As I'm sure you are aware it is highly flexible depending on the thickness, and in this case the vertical chassis plates provide adequate flex to nearly eliminate fatigue.
But I do need to work on better lower link mounting... ideas are much appreciated
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